Starting phenix.real_space_refine on Sat May 10 00:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8a_44336/05_2025/9b8a_44336.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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 15 5.16 5 C 2687 2.51 5 N 767 2.21 5 O 851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4320 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4320 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 531} Chain breaks: 1 Time building chain proxies: 3.56, per 1000 atoms: 0.82 Number of scatterers: 4320 At special positions: 0 Unit cell: (68.04, 59.4, 120.96, 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 15 16.00 O 851 8.00 N 767 7.00 C 2687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 851 " - pdb=" SG CYS A 856 " distance=2.03 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: 1.12 Conformation dependent library (CDL) restraints added in 568.7 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 30.9% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 602 through 615 removed outlier: 3.975A pdb=" N ALA A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 removed outlier: 3.673A pdb=" N ARG A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.665A pdb=" N SER A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 684 Processing helix chain 'A' and resid 686 through 704 removed outlier: 3.723A pdb=" N ALA A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'A' and resid 707 through 725 Processing helix chain 'A' and resid 726 through 741 Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 1069 through 1073 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1153 through 1157 Processing sheet with id=AA1, first strand: chain 'A' and resid 928 through 929 removed outlier: 5.377A pdb=" N GLY A 941 " --> pdb=" O LYS A 973 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 973 " --> pdb=" O GLY A 941 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY A 972 " --> pdb=" O GLU A 976 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 999 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 993 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A1054 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN A 862 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 869 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N VAL A 894 " --> pdb=" O PRO A 917 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 849 Processing sheet with id=AA3, first strand: chain 'A' and resid 1064 through 1065 286 hydrogen bonds defined for protein. 819 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: 1.51 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1465 1.34 - 1.46: 990 1.46 - 1.58: 1942 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4425 Sorted by residual: bond pdb=" N SER A 861 " pdb=" CA SER A 861 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.34e+00 bond pdb=" N ASP A 764 " pdb=" CA ASP A 764 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.37e-02 5.33e+03 8.23e+00 bond pdb=" N GLY A1002 " pdb=" CA GLY A1002 " ideal model delta sigma weight residual 1.447 1.475 -0.029 1.01e-02 9.80e+03 8.08e+00 bond pdb=" N ASP A 765 " pdb=" CA ASP A 765 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.69e+00 bond pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.35e+00 ... (remaining 4420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5767 1.41 - 2.81: 205 2.81 - 4.22: 40 4.22 - 5.62: 6 5.62 - 7.03: 3 Bond angle restraints: 6021 Sorted by residual: angle pdb=" CA ASP A 764 " pdb=" CB ASP A 764 " pdb=" CG ASP A 764 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.00e+00 1.00e+00 1.40e+01 angle pdb=" CA ASP A 611 " pdb=" CB ASP A 611 " pdb=" CG ASP A 611 " ideal model delta sigma weight residual 112.60 116.14 -3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA GLN A 691 " pdb=" CB GLN A 691 " pdb=" CG GLN A 691 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG A 860 " pdb=" CB ARG A 860 " pdb=" CG ARG A 860 " ideal model delta sigma weight residual 114.10 108.02 6.08 2.00e+00 2.50e-01 9.23e+00 angle pdb=" CA GLY A1002 " pdb=" C GLY A1002 " pdb=" O GLY A1002 " ideal model delta sigma weight residual 121.46 118.00 3.46 1.15e+00 7.56e-01 9.04e+00 ... (remaining 6016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2380 17.39 - 34.78: 154 34.78 - 52.17: 38 52.17 - 69.56: 12 69.56 - 86.95: 6 Dihedral angle restraints: 2590 sinusoidal: 1006 harmonic: 1584 Sorted by residual: dihedral pdb=" CG ARG A 915 " pdb=" CD ARG A 915 " pdb=" NE ARG A 915 " pdb=" CZ ARG A 915 " ideal model delta sinusoidal sigma weight residual -180.00 -135.07 -44.93 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB MET A 984 " pdb=" CG MET A 984 " pdb=" SD MET A 984 " pdb=" CE MET A 984 " ideal model delta sinusoidal sigma weight residual -180.00 -125.31 -54.69 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA ASP A 803 " pdb=" C ASP A 803 " pdb=" N LEU A 804 " pdb=" CA LEU A 804 " ideal model delta harmonic sigma weight residual -180.00 -164.83 -15.17 0 5.00e+00 4.00e-02 9.21e+00 ... (remaining 2587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 429 0.034 - 0.068: 140 0.068 - 0.103: 37 0.103 - 0.137: 19 0.137 - 0.171: 4 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA MET A 887 " pdb=" N MET A 887 " pdb=" C MET A 887 " pdb=" CB MET A 887 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA GLU A 709 " pdb=" N GLU A 709 " pdb=" C GLU A 709 " pdb=" CB GLU A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA GLN A 862 " pdb=" N GLN A 862 " pdb=" C GLN A 862 " pdb=" CB GLN A 862 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 626 not shown) Planarity restraints: 796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1035 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO A1036 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1036 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1036 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 905 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 906 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 906 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 906 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1073 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A1074 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1074 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1074 " -0.018 5.00e-02 4.00e+02 ... (remaining 793 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 354 2.74 - 3.28: 4131 3.28 - 3.82: 7046 3.82 - 4.36: 8215 4.36 - 4.90: 15117 Nonbonded interactions: 34863 Sorted by model distance: nonbonded pdb=" OG SER A1053 " pdb=" OG1 THR A1097 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP A 611 " pdb=" OH TYR A 626 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP A 954 " pdb=" OH TYR A 988 " model vdw 2.307 3.040 nonbonded pdb=" N THR A 798 " pdb=" OG SER A 802 " model vdw 2.408 3.120 nonbonded pdb=" O ASN A 751 " pdb=" OG1 THR A 755 " model vdw 2.422 3.040 ... (remaining 34858 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.720 Find NCS groups from input model: 0.050 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: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4426 Z= 0.250 Angle : 0.640 7.026 6023 Z= 0.404 Chirality : 0.041 0.171 629 Planarity : 0.004 0.049 796 Dihedral : 13.806 86.950 1579 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.11 % Allowed : 5.12 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.35), residues: 550 helix: 1.14 (0.41), residues: 156 sheet: 1.39 (0.33), residues: 209 loop : -0.35 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1140 HIS 0.001 0.000 HIS A 807 PHE 0.007 0.001 PHE A 925 TYR 0.008 0.001 TYR A1132 ARG 0.007 0.000 ARG A 874 Details of bonding type rmsd hydrogen bonds : bond 0.14250 ( 286) hydrogen bonds : angle 5.97857 ( 819) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.14808 ( 2) covalent geometry : bond 0.00357 ( 4425) covalent geometry : angle 0.64039 ( 6021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 859 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (p0) REVERT: A 1064 MET cc_start: 0.7732 (tpt) cc_final: 0.7402 (tpp) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.1908 time to fit residues: 12.9589 Evaluate side-chains 49 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 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 = 0.3592 r_free = 0.3592 target = 0.125540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105287 restraints weight = 6663.345| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.95 r_work: 0.3237 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4426 Z= 0.200 Angle : 0.577 5.516 6023 Z= 0.315 Chirality : 0.042 0.142 629 Planarity : 0.004 0.038 796 Dihedral : 5.264 54.775 619 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 7.35 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 550 helix: 1.40 (0.41), residues: 156 sheet: 1.13 (0.32), residues: 222 loop : -0.26 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1056 HIS 0.004 0.001 HIS A1128 PHE 0.011 0.002 PHE A 925 TYR 0.013 0.002 TYR A1135 ARG 0.004 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 286) hydrogen bonds : angle 5.19666 ( 819) SS BOND : bond 0.00615 ( 1) SS BOND : angle 0.78471 ( 2) covalent geometry : bond 0.00461 ( 4425) covalent geometry : angle 0.57710 ( 6021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 874 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7868 (ttp-110) REVERT: A 1064 MET cc_start: 0.7934 (tpt) cc_final: 0.7544 (tpp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1806 time to fit residues: 11.5786 Evaluate side-chains 45 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107063 restraints weight = 6672.524| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.96 r_work: 0.3242 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4426 Z= 0.146 Angle : 0.514 4.565 6023 Z= 0.282 Chirality : 0.041 0.143 629 Planarity : 0.004 0.038 796 Dihedral : 5.121 56.844 615 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.00 % Allowed : 7.13 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.35), residues: 550 helix: 1.64 (0.41), residues: 156 sheet: 1.07 (0.32), residues: 222 loop : -0.39 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1008 HIS 0.003 0.001 HIS A1128 PHE 0.009 0.001 PHE A 823 TYR 0.009 0.001 TYR A 801 ARG 0.004 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 286) hydrogen bonds : angle 5.01443 ( 819) SS BOND : bond 0.00391 ( 1) SS BOND : angle 0.58751 ( 2) covalent geometry : bond 0.00336 ( 4425) covalent geometry : angle 0.51362 ( 6021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7384 (tmt170) REVERT: A 864 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8153 (t0) REVERT: A 874 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7889 (ttp-110) REVERT: A 1064 MET cc_start: 0.7992 (tpt) cc_final: 0.7555 (tpp) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.2032 time to fit residues: 13.9568 Evaluate side-chains 51 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.127264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106900 restraints weight = 6659.002| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.94 r_work: 0.3243 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4426 Z= 0.142 Angle : 0.505 4.558 6023 Z= 0.277 Chirality : 0.040 0.145 629 Planarity : 0.004 0.037 796 Dihedral : 5.136 58.614 615 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 8.24 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.35), residues: 550 helix: 1.75 (0.41), residues: 156 sheet: 1.11 (0.32), residues: 218 loop : -0.50 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 PHE 0.008 0.001 PHE A 823 TYR 0.009 0.001 TYR A1135 ARG 0.005 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 286) hydrogen bonds : angle 4.94267 ( 819) SS BOND : bond 0.00387 ( 1) SS BOND : angle 0.41068 ( 2) covalent geometry : bond 0.00326 ( 4425) covalent geometry : angle 0.50547 ( 6021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7406 (tmt170) REVERT: A 864 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 874 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7892 (ttp-110) REVERT: A 1064 MET cc_start: 0.8011 (tpt) cc_final: 0.7598 (tpp) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.1957 time to fit residues: 13.4137 Evaluate side-chains 51 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.126209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105473 restraints weight = 6746.662| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.04 r_work: 0.3217 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4426 Z= 0.176 Angle : 0.527 4.488 6023 Z= 0.289 Chirality : 0.041 0.145 629 Planarity : 0.004 0.037 796 Dihedral : 5.224 59.601 615 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.67 % Allowed : 9.13 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.98 (0.35), residues: 550 helix: 1.63 (0.41), residues: 156 sheet: 1.03 (0.32), residues: 219 loop : -0.71 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 PHE 0.008 0.001 PHE A 823 TYR 0.010 0.001 TYR A1135 ARG 0.005 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 286) hydrogen bonds : angle 4.98105 ( 819) SS BOND : bond 0.00518 ( 1) SS BOND : angle 0.48991 ( 2) covalent geometry : bond 0.00408 ( 4425) covalent geometry : angle 0.52722 ( 6021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 864 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 874 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7966 (ttp-110) REVERT: A 1064 MET cc_start: 0.8025 (tpt) cc_final: 0.7613 (tpp) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.1898 time to fit residues: 12.4876 Evaluate side-chains 48 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.125500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104161 restraints weight = 6635.610| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.08 r_work: 0.3194 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4426 Z= 0.136 Angle : 0.507 4.456 6023 Z= 0.279 Chirality : 0.040 0.147 629 Planarity : 0.004 0.036 796 Dihedral : 5.147 59.746 615 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.78 % Allowed : 10.91 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.35), residues: 550 helix: 1.72 (0.41), residues: 156 sheet: 1.05 (0.33), residues: 217 loop : -0.75 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 939 HIS 0.002 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.008 0.001 TYR A1135 ARG 0.002 0.000 ARG A1040 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 286) hydrogen bonds : angle 4.86499 ( 819) SS BOND : bond 0.00381 ( 1) SS BOND : angle 0.39958 ( 2) covalent geometry : bond 0.00313 ( 4425) covalent geometry : angle 0.50712 ( 6021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7393 (tmt170) REVERT: A 864 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8073 (t0) REVERT: A 874 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7868 (ttp-110) REVERT: A 1064 MET cc_start: 0.8011 (tpt) cc_final: 0.7567 (tpp) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.2079 time to fit residues: 12.9961 Evaluate side-chains 47 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.125321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103993 restraints weight = 6621.180| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.10 r_work: 0.3193 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4426 Z= 0.140 Angle : 0.508 4.778 6023 Z= 0.280 Chirality : 0.040 0.147 629 Planarity : 0.004 0.036 796 Dihedral : 5.124 59.503 615 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.67 % Allowed : 10.69 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.35), residues: 550 helix: 1.70 (0.41), residues: 156 sheet: 1.06 (0.33), residues: 217 loop : -0.75 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.009 0.001 TYR A1135 ARG 0.006 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 286) hydrogen bonds : angle 4.81951 ( 819) SS BOND : bond 0.00405 ( 1) SS BOND : angle 0.42972 ( 2) covalent geometry : bond 0.00324 ( 4425) covalent geometry : angle 0.50848 ( 6021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7443 (tmt170) REVERT: A 660 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7316 (tp) REVERT: A 864 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8030 (t0) REVERT: A 874 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7882 (ttp-110) REVERT: A 1064 MET cc_start: 0.8012 (tpt) cc_final: 0.7566 (tpp) outliers start: 12 outliers final: 10 residues processed: 54 average time/residue: 0.2022 time to fit residues: 13.5377 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.124384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103234 restraints weight = 6610.013| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.03 r_work: 0.3196 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4426 Z= 0.156 Angle : 0.523 5.141 6023 Z= 0.287 Chirality : 0.040 0.146 629 Planarity : 0.004 0.036 796 Dihedral : 5.143 59.398 615 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.12 % Allowed : 10.47 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.97 (0.35), residues: 550 helix: 1.69 (0.41), residues: 156 sheet: 1.02 (0.33), residues: 217 loop : -0.77 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 939 HIS 0.003 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.009 0.001 TYR A1135 ARG 0.002 0.000 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 286) hydrogen bonds : angle 4.85430 ( 819) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.46575 ( 2) covalent geometry : bond 0.00363 ( 4425) covalent geometry : angle 0.52328 ( 6021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7407 (tmt170) REVERT: A 645 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 660 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7339 (tp) REVERT: A 864 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8047 (t0) REVERT: A 874 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7923 (ttp-110) REVERT: A 1038 MET cc_start: 0.8204 (tmm) cc_final: 0.7851 (tmm) REVERT: A 1064 MET cc_start: 0.7958 (tpt) cc_final: 0.7517 (tpp) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.2066 time to fit residues: 13.9685 Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.125804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104545 restraints weight = 6635.131| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.09 r_work: 0.3205 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4426 Z= 0.124 Angle : 0.503 6.485 6023 Z= 0.277 Chirality : 0.039 0.148 629 Planarity : 0.004 0.034 796 Dihedral : 5.062 58.910 615 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.67 % Allowed : 10.69 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 550 helix: 1.75 (0.41), residues: 156 sheet: 1.05 (0.33), residues: 217 loop : -0.73 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 793 HIS 0.002 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.008 0.001 TYR A1135 ARG 0.007 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 286) hydrogen bonds : angle 4.78170 ( 819) SS BOND : bond 0.00342 ( 1) SS BOND : angle 0.41127 ( 2) covalent geometry : bond 0.00285 ( 4425) covalent geometry : angle 0.50289 ( 6021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8417 (tpp80) cc_final: 0.7494 (tmt170) REVERT: A 660 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7398 (tp) REVERT: A 864 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8077 (t0) REVERT: A 874 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7852 (ttp-110) REVERT: A 1038 MET cc_start: 0.8198 (tmm) cc_final: 0.7846 (tmm) REVERT: A 1064 MET cc_start: 0.7958 (tpt) cc_final: 0.7511 (tpp) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.1998 time to fit residues: 13.0018 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.124357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103123 restraints weight = 6566.428| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.04 r_work: 0.3195 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4426 Z= 0.168 Angle : 0.533 6.029 6023 Z= 0.292 Chirality : 0.040 0.145 629 Planarity : 0.004 0.034 796 Dihedral : 5.164 59.203 615 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.12 % Allowed : 10.91 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.96 (0.35), residues: 550 helix: 1.72 (0.41), residues: 156 sheet: 1.01 (0.33), residues: 218 loop : -0.80 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 939 HIS 0.003 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.010 0.001 TYR A1135 ARG 0.002 0.000 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 286) hydrogen bonds : angle 4.86263 ( 819) SS BOND : bond 0.00497 ( 1) SS BOND : angle 0.48695 ( 2) covalent geometry : bond 0.00393 ( 4425) covalent geometry : angle 0.53333 ( 6021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7432 (tmt170) REVERT: A 660 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7340 (tt) REVERT: A 864 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8064 (t0) REVERT: A 874 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7858 (ttp-110) REVERT: A 1064 MET cc_start: 0.7968 (tpt) cc_final: 0.7525 (tpp) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1954 time to fit residues: 12.7979 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 TRP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.125956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104653 restraints weight = 6593.947| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4426 Z= 0.128 Angle : 0.507 5.883 6023 Z= 0.279 Chirality : 0.040 0.147 629 Planarity : 0.004 0.036 796 Dihedral : 5.084 58.736 615 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.67 % Allowed : 11.58 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.99 (0.35), residues: 550 helix: 1.78 (0.41), residues: 155 sheet: 1.04 (0.33), residues: 217 loop : -0.81 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1056 HIS 0.002 0.001 HIS A1128 PHE 0.007 0.001 PHE A 823 TYR 0.011 0.001 TYR A 619 ARG 0.008 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 286) hydrogen bonds : angle 4.79017 ( 819) SS BOND : bond 0.00367 ( 1) SS BOND : angle 0.41640 ( 2) covalent geometry : bond 0.00295 ( 4425) covalent geometry : angle 0.50742 ( 6021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.60 seconds wall clock time: 46 minutes 24.17 seconds (2784.17 seconds total)