Starting phenix.real_space_refine on Thu Jul 24 05:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gik_51373/07_2025/9gik_51373.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gik_51373/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gik_51373/07_2025/9gik_51373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gik_51373/07_2025/9gik_51373.map" model { file = "/net/cci-nas-00/data/ceres_data/9gik_51373/07_2025/9gik_51373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gik_51373/07_2025/9gik_51373.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.01, per 1000 atoms: 0.75 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: 1.47 Conformation dependent library (CDL) restraints added in 586.3 milliseconds 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: 0.60 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: 1.47 Time building geometry restraints manager: 1.48 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (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 TRP 0.006 0.001 TRP A 864 HIS 0.002 0.001 HIS A 686 PHE 0.007 0.001 PHE A 905 TYR 0.011 0.001 TYR A 152 ARG 0.002 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.23781 ( 203) hydrogen bonds : angle 7.96457 ( 534) covalent geometry : bond 0.00270 ( 5465) covalent geometry : angle 0.50876 ( 7395) *********************** 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 : 0.582 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: 0.1827 time to fit residues: 23.5155 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 : 0.581 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.0070 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 801 GLN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095832 restraints weight = 9431.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096764 restraints weight = 6882.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097147 restraints weight = 5541.507| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1535 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= 0.145 Angle : 0.572 9.917 7395 Z= 0.285 Chirality : 0.042 0.136 764 Planarity : 0.004 0.043 968 Dihedral : 4.404 45.937 715 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.23 % Allowed : 9.08 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 633 helix: 0.72 (0.36), residues: 197 sheet: -0.98 (0.45), residues: 130 loop : -0.43 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.003 0.001 HIS A 920 PHE 0.011 0.001 PHE A 128 TYR 0.009 0.001 TYR A 581 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 203) hydrogen bonds : angle 5.75477 ( 534) covalent geometry : bond 0.00339 ( 5465) covalent geometry : angle 0.57181 ( 7395) *********************** 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 78 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.573 Fit side-chains REVERT: A 708 ASP cc_start: 0.7721 (t0) cc_final: 0.7412 (t0) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.1407 time to fit residues: 14.4626 Evaluate side-chains 66 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094544 restraints weight = 9453.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.095022 restraints weight = 6966.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095811 restraints weight = 5769.518| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5465 Z= 0.151 Angle : 0.542 8.397 7395 Z= 0.272 Chirality : 0.041 0.132 764 Planarity : 0.004 0.029 968 Dihedral : 4.556 48.081 715 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 8.56 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.33), residues: 633 helix: 0.71 (0.36), residues: 199 sheet: -1.10 (0.46), residues: 124 loop : -0.43 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.006 0.001 HIS A 87 PHE 0.009 0.001 PHE A 649 TYR 0.009 0.001 TYR A 581 ARG 0.002 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 203) hydrogen bonds : angle 5.37700 ( 534) covalent geometry : bond 0.00360 ( 5465) covalent geometry : angle 0.54247 ( 7395) *********************** 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 : 0.585 Fit side-chains revert: symmetry clash REVERT: A 708 ASP cc_start: 0.7947 (t0) cc_final: 0.7587 (t0) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1330 time to fit residues: 14.3957 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 : 0.575 ------------------------------------------------------------------------------- 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 12 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 A 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092458 restraints weight = 9673.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092944 restraints weight = 7113.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093369 restraints weight = 6056.065| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5465 Z= 0.214 Angle : 0.572 7.126 7395 Z= 0.291 Chirality : 0.043 0.138 764 Planarity : 0.004 0.029 968 Dihedral : 4.813 52.993 713 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.74 % Allowed : 9.93 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.33), residues: 633 helix: 0.59 (0.36), residues: 199 sheet: -1.35 (0.45), residues: 121 loop : -0.54 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.003 0.001 HIS A 549 PHE 0.015 0.002 PHE A 128 TYR 0.011 0.001 TYR A 581 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 203) hydrogen bonds : angle 5.26913 ( 534) covalent geometry : bond 0.00515 ( 5465) covalent geometry : angle 0.57215 ( 7395) *********************** 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 73 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.651 Fit side-chains REVERT: A 708 ASP cc_start: 0.8035 (t0) cc_final: 0.7650 (t0) REVERT: A 757 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8540 (mp) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.1449 time to fit residues: 14.4618 Evaluate side-chains 63 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095419 restraints weight = 9461.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095703 restraints weight = 6993.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096270 restraints weight = 6060.863| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2275 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 : 0.517 7.447 7395 Z= 0.264 Chirality : 0.041 0.147 764 Planarity : 0.004 0.029 968 Dihedral : 4.730 54.198 713 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.23 % Allowed : 11.64 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 633 helix: 0.82 (0.37), residues: 199 sheet: -1.19 (0.46), residues: 116 loop : -0.53 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 864 HIS 0.002 0.001 HIS A 549 PHE 0.012 0.001 PHE A 128 TYR 0.007 0.001 TYR A 736 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 203) hydrogen bonds : angle 5.01182 ( 534) covalent geometry : bond 0.00285 ( 5465) covalent geometry : angle 0.51658 ( 7395) *********************** 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 68 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.671 Fit side-chains REVERT: A 708 ASP cc_start: 0.7980 (t0) cc_final: 0.7618 (t0) REVERT: A 757 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (mp) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.1400 time to fit residues: 13.3034 Evaluate side-chains 65 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 655 MET 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 18 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095065 restraints weight = 9397.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095315 restraints weight = 6965.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095747 restraints weight = 6094.023| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5465 Z= 0.149 Angle : 0.525 6.594 7395 Z= 0.269 Chirality : 0.041 0.141 764 Planarity : 0.004 0.028 968 Dihedral : 4.762 55.217 713 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.91 % Allowed : 10.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.33), residues: 633 helix: 0.79 (0.37), residues: 199 sheet: -0.99 (0.47), residues: 112 loop : -0.63 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 864 HIS 0.003 0.001 HIS A 549 PHE 0.009 0.001 PHE A 905 TYR 0.009 0.001 TYR A 581 ARG 0.002 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 203) hydrogen bonds : angle 4.95918 ( 534) covalent geometry : bond 0.00360 ( 5465) covalent geometry : angle 0.52534 ( 7395) *********************** 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 73 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.601 Fit side-chains REVERT: A 708 ASP cc_start: 0.8008 (t0) cc_final: 0.7633 (t0) REVERT: A 757 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8574 (mp) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.1377 time to fit residues: 13.6520 Evaluate side-chains 66 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 655 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.121328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093699 restraints weight = 9499.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094088 restraints weight = 6933.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094711 restraints weight = 5941.895| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5465 Z= 0.152 Angle : 0.530 7.902 7395 Z= 0.271 Chirality : 0.041 0.143 764 Planarity : 0.004 0.029 968 Dihedral : 4.789 56.476 713 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.57 % Allowed : 11.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.33), residues: 633 helix: 0.78 (0.37), residues: 199 sheet: -1.00 (0.48), residues: 112 loop : -0.64 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 864 HIS 0.003 0.001 HIS A 549 PHE 0.011 0.001 PHE A 131 TYR 0.008 0.001 TYR A 581 ARG 0.001 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 203) hydrogen bonds : angle 4.93044 ( 534) covalent geometry : bond 0.00367 ( 5465) covalent geometry : angle 0.52958 ( 7395) *********************** 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 70 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.604 Fit side-chains REVERT: A 150 MET cc_start: 0.8351 (mmm) cc_final: 0.8142 (mtp) REVERT: A 708 ASP cc_start: 0.7953 (t0) cc_final: 0.7578 (t0) REVERT: A 757 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8586 (mp) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1297 time to fit residues: 12.6434 Evaluate side-chains 66 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 655 MET 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 40 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 A 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094240 restraints weight = 9612.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095620 restraints weight = 7691.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096310 restraints weight = 5828.396| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5465 Z= 0.111 Angle : 0.513 7.614 7395 Z= 0.259 Chirality : 0.040 0.137 764 Planarity : 0.004 0.032 968 Dihedral : 4.700 56.805 713 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.40 % Allowed : 12.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.34), residues: 633 helix: 0.87 (0.37), residues: 200 sheet: -0.94 (0.48), residues: 112 loop : -0.59 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 910 HIS 0.002 0.000 HIS A 549 PHE 0.009 0.001 PHE A 905 TYR 0.006 0.001 TYR A 736 ARG 0.001 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 203) hydrogen bonds : angle 4.80854 ( 534) covalent geometry : bond 0.00265 ( 5465) covalent geometry : angle 0.51253 ( 7395) *********************** 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 73 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.655 Fit side-chains REVERT: A 708 ASP cc_start: 0.8059 (t0) cc_final: 0.7641 (t0) REVERT: A 757 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8533 (mp) outliers start: 14 outliers final: 11 residues processed: 70 average time/residue: 0.1356 time to fit residues: 13.6654 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 : 0.650 ------------------------------------------------------------------------------- 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 655 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.0040 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.0030 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094339 restraints weight = 9627.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095459 restraints weight = 7855.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096137 restraints weight = 5938.532| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2615 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= 0.110 Angle : 0.521 7.646 7395 Z= 0.261 Chirality : 0.040 0.137 764 Planarity : 0.004 0.037 968 Dihedral : 4.661 56.866 713 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.40 % Allowed : 12.67 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.34), residues: 633 helix: 0.91 (0.37), residues: 200 sheet: -0.91 (0.49), residues: 112 loop : -0.57 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 864 HIS 0.002 0.000 HIS A 549 PHE 0.009 0.001 PHE A 905 TYR 0.006 0.001 TYR A 581 ARG 0.001 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 203) hydrogen bonds : angle 4.75660 ( 534) covalent geometry : bond 0.00265 ( 5465) covalent geometry : angle 0.52070 ( 7395) *********************** 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 70 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.601 Fit side-chains REVERT: A 708 ASP cc_start: 0.8057 (t0) cc_final: 0.7644 (t0) REVERT: A 757 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8529 (mp) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.1326 time to fit residues: 13.0378 Evaluate side-chains 65 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 780 THR Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.122429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094999 restraints weight = 9707.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095683 restraints weight = 7124.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096499 restraints weight = 5926.325| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2651 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= 0.105 Angle : 0.518 7.646 7395 Z= 0.261 Chirality : 0.040 0.136 764 Planarity : 0.004 0.035 968 Dihedral : 4.643 56.946 713 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.05 % Allowed : 13.18 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.34), residues: 633 helix: 0.97 (0.37), residues: 200 sheet: -0.84 (0.49), residues: 112 loop : -0.55 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 864 HIS 0.002 0.000 HIS A 549 PHE 0.010 0.001 PHE A 905 TYR 0.006 0.001 TYR A 581 ARG 0.001 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 203) hydrogen bonds : angle 4.71290 ( 534) covalent geometry : bond 0.00250 ( 5465) covalent geometry : angle 0.51815 ( 7395) ********************** 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 68 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.586 Fit side-chains REVERT: A 708 ASP cc_start: 0.8025 (t0) cc_final: 0.7611 (t0) REVERT: A 757 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8576 (mp) outliers start: 12 outliers final: 11 residues processed: 66 average time/residue: 0.1358 time to fit residues: 12.9762 Evaluate side-chains 65 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 780 THR Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094675 restraints weight = 9656.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095263 restraints weight = 7151.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096130 restraints weight = 5870.672| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5465 Z= 0.125 Angle : 0.522 7.519 7395 Z= 0.263 Chirality : 0.040 0.138 764 Planarity : 0.004 0.037 968 Dihedral : 4.684 57.260 713 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.23 % Allowed : 13.01 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.34), residues: 633 helix: 0.97 (0.37), residues: 200 sheet: -0.85 (0.49), residues: 112 loop : -0.58 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 864 HIS 0.002 0.000 HIS A 549 PHE 0.011 0.001 PHE A 905 TYR 0.007 0.001 TYR A 581 ARG 0.001 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 203) hydrogen bonds : angle 4.72251 ( 534) covalent geometry : bond 0.00304 ( 5465) covalent geometry : angle 0.52229 ( 7395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.56 seconds wall clock time: 33 minutes 35.99 seconds (2015.99 seconds total)