Starting phenix.real_space_refine on Thu Mar 6 01:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8a_44336/03_2025/9b8a_44336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8a_44336/03_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_44336/03_2025/9b8a_44336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8a_44336/03_2025/9b8a_44336.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8a_44336/03_2025/9b8a_44336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8a_44336/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.04, per 1000 atoms: 0.94 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: 1.05 Conformation dependent library (CDL) restraints added in 522.0 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: 0.50 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: 1.38 Time building geometry restraints manager: 1.26 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- 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 4425 Z= 0.233 Angle : 0.640 7.026 6021 Z= 0.405 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 *********************** 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 : 0.650 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: 0.1864 time to fit residues: 12.6993 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 : 0.509 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.125542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105273 restraints weight = 6663.307| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.96 r_work: 0.3236 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 4425 Z= 0.300 Angle : 0.577 5.514 6021 Z= 0.315 Chirality : 0.042 0.142 629 Planarity : 0.004 0.038 796 Dihedral : 5.264 54.776 619 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 *********************** 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 : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 874 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7860 (ttp-110) REVERT: A 1064 MET cc_start: 0.7937 (tpt) cc_final: 0.7546 (tpp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1872 time to fit residues: 12.0763 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 : 0.444 ------------------------------------------------------------------------------- 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: 0.5980 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.128461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107724 restraints weight = 6635.390| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.01 r_work: 0.3254 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4425 Z= 0.171 Angle : 0.493 4.588 6021 Z= 0.271 Chirality : 0.040 0.144 629 Planarity : 0.004 0.037 796 Dihedral : 5.032 56.191 615 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 7.13 % Favored : 91.09 % 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: 1.25 (0.35), residues: 550 helix: 1.70 (0.41), residues: 156 sheet: 1.13 (0.32), residues: 222 loop : -0.33 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1128 PHE 0.008 0.001 PHE A 823 TYR 0.007 0.001 TYR A 801 ARG 0.005 0.000 ARG A 623 *********************** 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: 8 poor density : 48 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7395 (tmt170) REVERT: A 864 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8147 (t0) REVERT: A 874 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7910 (ttp-110) REVERT: A 1064 MET cc_start: 0.8002 (tpt) cc_final: 0.7573 (tpp) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1937 time to fit residues: 13.2844 Evaluate side-chains 48 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.125821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104762 restraints weight = 6698.552| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.08 r_work: 0.3209 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4425 Z= 0.285 Angle : 0.546 4.520 6021 Z= 0.299 Chirality : 0.041 0.143 629 Planarity : 0.004 0.037 796 Dihedral : 5.022 58.251 613 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.45 % Allowed : 7.80 % Favored : 89.76 % 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: 1.07 (0.35), residues: 550 helix: 1.66 (0.41), residues: 156 sheet: 1.07 (0.32), residues: 219 loop : -0.58 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 939 HIS 0.003 0.001 HIS A1128 PHE 0.009 0.001 PHE A 925 TYR 0.012 0.001 TYR A1135 ARG 0.004 0.000 ARG A 623 *********************** 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 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 864 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 874 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7925 (ttp-110) REVERT: A 1064 MET cc_start: 0.8028 (tpt) cc_final: 0.7610 (tpp) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1848 time to fit residues: 12.7264 Evaluate side-chains 49 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 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 = 0.3590 r_free = 0.3590 target = 0.125843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105063 restraints weight = 6732.154| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.04 r_work: 0.3217 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4425 Z= 0.267 Angle : 0.530 4.426 6021 Z= 0.291 Chirality : 0.041 0.145 629 Planarity : 0.004 0.037 796 Dihedral : 5.034 59.689 613 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.00 % Allowed : 9.58 % Favored : 88.42 % 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: 1.61 (0.41), residues: 156 sheet: 1.03 (0.32), residues: 218 loop : -0.67 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 939 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 *********************** 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: 9 poor density : 44 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7349 (tmt170) REVERT: A 864 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 874 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7932 (ttp-110) REVERT: A 1064 MET cc_start: 0.8019 (tpt) cc_final: 0.7615 (tpp) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.2092 time to fit residues: 13.4436 Evaluate side-chains 47 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.127833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107075 restraints weight = 6689.404| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.06 r_work: 0.3238 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4425 Z= 0.173 Angle : 0.496 4.519 6021 Z= 0.274 Chirality : 0.040 0.147 629 Planarity : 0.004 0.036 796 Dihedral : 4.882 59.631 613 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.45 % Allowed : 10.24 % 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: 1.07 (0.35), residues: 550 helix: 1.78 (0.41), residues: 156 sheet: 1.06 (0.33), residues: 217 loop : -0.69 (0.46), 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 0.007 0.001 TYR A1135 ARG 0.002 0.000 ARG A1040 *********************** 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 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7400 (tmt170) REVERT: A 864 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8110 (t0) REVERT: A 874 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7928 (ttp-110) REVERT: A 1064 MET cc_start: 0.8006 (tpt) cc_final: 0.7583 (tpp) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1779 time to fit residues: 11.9659 Evaluate side-chains 50 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 1000 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: 0.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103824 restraints weight = 6635.525| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.09 r_work: 0.3197 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4425 Z= 0.224 Angle : 0.518 4.724 6021 Z= 0.286 Chirality : 0.040 0.146 629 Planarity : 0.004 0.037 796 Dihedral : 4.928 59.657 613 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 10.69 % Favored : 86.86 % 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: 1.75 (0.41), residues: 156 sheet: 1.02 (0.33), residues: 217 loop : -0.73 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.007 0.000 ARG A 623 *********************** 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 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8403 (tpp80) cc_final: 0.7440 (tmt170) REVERT: A 660 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7332 (tt) REVERT: A 864 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8047 (t0) REVERT: A 874 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7906 (ttp-110) REVERT: A 1038 MET cc_start: 0.8259 (tmm) cc_final: 0.7923 (tmm) REVERT: A 1064 MET cc_start: 0.8022 (tpt) cc_final: 0.7577 (tpp) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.2089 time to fit residues: 13.5258 Evaluate side-chains 50 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103283 restraints weight = 6623.248| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.04 r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4425 Z= 0.245 Angle : 0.527 5.158 6021 Z= 0.290 Chirality : 0.040 0.147 629 Planarity : 0.004 0.037 796 Dihedral : 4.939 59.735 613 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.90 % Allowed : 10.24 % Favored : 86.86 % 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: 1.70 (0.41), residues: 156 sheet: 0.98 (0.33), residues: 217 loop : -0.74 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 A1040 *********************** 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: 13 poor density : 42 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7408 (tmt170) REVERT: A 645 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 660 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7339 (tt) REVERT: A 864 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8051 (t0) REVERT: A 874 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7936 (ttp-110) REVERT: A 1064 MET cc_start: 0.7997 (tpt) cc_final: 0.7559 (tpp) outliers start: 13 outliers final: 11 residues processed: 53 average time/residue: 0.1847 time to fit residues: 12.3649 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.126366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104960 restraints weight = 6649.270| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.11 r_work: 0.3213 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4425 Z= 0.175 Angle : 0.497 6.546 6021 Z= 0.274 Chirality : 0.039 0.147 629 Planarity : 0.004 0.037 796 Dihedral : 4.822 59.111 613 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.67 % Allowed : 10.24 % Favored : 87.08 % 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: 1.07 (0.35), residues: 550 helix: 1.79 (0.41), residues: 156 sheet: 1.06 (0.33), residues: 217 loop : -0.71 (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 0.007 0.001 TYR A1135 ARG 0.007 0.000 ARG A 623 *********************** 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 58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8394 (tpp80) cc_final: 0.7471 (tmt170) REVERT: A 645 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 660 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 864 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8057 (t0) REVERT: A 874 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7840 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.2441 time to fit residues: 17.9386 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 : 0.763 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.0470 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 52 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.127818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106571 restraints weight = 6461.682| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.06 r_work: 0.3233 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4425 Z= 0.150 Angle : 0.491 6.222 6021 Z= 0.270 Chirality : 0.039 0.147 629 Planarity : 0.004 0.038 796 Dihedral : 4.745 58.798 613 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.90 % Allowed : 10.69 % 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: 1.16 (0.36), residues: 550 helix: 1.91 (0.41), residues: 156 sheet: 1.09 (0.33), residues: 217 loop : -0.67 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1058 PHE 0.007 0.001 PHE A 823 TYR 0.007 0.001 TYR A1132 ARG 0.003 0.000 ARG A1040 ********************** 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 57 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7446 (tmt170) REVERT: A 660 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 864 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8026 (t0) REVERT: A 874 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7801 (ttp-110) REVERT: A 1130 LEU cc_start: 0.9301 (pp) cc_final: 0.9060 (pp) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.3405 time to fit residues: 24.8463 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103905 restraints weight = 6606.395| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.11 r_work: 0.3202 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4425 Z= 0.231 Angle : 0.530 5.847 6021 Z= 0.290 Chirality : 0.041 0.146 629 Planarity : 0.004 0.037 796 Dihedral : 4.870 59.007 613 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.90 % Allowed : 10.91 % Favored : 86.19 % 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: 1.04 (0.36), residues: 550 helix: 1.87 (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 0.009 0.001 TRP A 939 HIS 0.002 0.001 HIS A1128 PHE 0.011 0.001 PHE A 823 TYR 0.013 0.001 TYR A 619 ARG 0.007 0.000 ARG A 623 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.04 seconds wall clock time: 49 minutes 48.68 seconds (2988.68 seconds total)