Starting phenix.real_space_refine on Wed Sep 17 04:43:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8a_44336/09_2025/9b8a_44336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8a_44336/09_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_44336/09_2025/9b8a_44336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8a_44336/09_2025/9b8a_44336.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8a_44336/09_2025/9b8a_44336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8a_44336/09_2025/9b8a_44336.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.32, per 1000 atoms: 0.31 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: 0.30 Conformation dependent library (CDL) restraints added in 172.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 0.73 Time building geometry restraints manager: 0.45 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.007 0.000 ARG A 874 TYR 0.008 0.001 TYR A1132 PHE 0.007 0.001 PHE A 925 TRP 0.018 0.002 TRP A1140 HIS 0.001 0.000 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4425) covalent geometry : angle 0.64039 ( 6021) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.14808 ( 2) hydrogen bonds : bond 0.14250 ( 286) hydrogen bonds : angle 5.97857 ( 819) *********************** 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 : 0.101 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: 0.0845 time to fit residues: 5.7472 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 : 0.117 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.128758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107763 restraints weight = 6661.825| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.07 r_work: 0.3269 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1139 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= 0.136 Angle : 0.524 5.710 6023 Z= 0.287 Chirality : 0.040 0.142 629 Planarity : 0.004 0.036 796 Dihedral : 5.011 52.265 619 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.34 % Allowed : 7.13 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.35), residues: 550 helix: 1.49 (0.41), residues: 156 sheet: 1.25 (0.32), residues: 222 loop : -0.11 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.009 0.001 TYR A1132 PHE 0.009 0.001 PHE A 823 TRP 0.009 0.001 TRP A 873 HIS 0.002 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4425) covalent geometry : angle 0.52404 ( 6021) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.57843 ( 2) hydrogen bonds : bond 0.03710 ( 286) hydrogen bonds : angle 5.09019 ( 819) *********************** 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 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 874 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7877 (ttp-110) REVERT: A 1064 MET cc_start: 0.7945 (tpt) cc_final: 0.7516 (tpp) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.0744 time to fit residues: 4.8587 Evaluate side-chains 45 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 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 = 0.3616 r_free = 0.3616 target = 0.127913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107130 restraints weight = 6661.201| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.02 r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1601 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= 0.151 Angle : 0.517 4.523 6023 Z= 0.283 Chirality : 0.041 0.141 629 Planarity : 0.004 0.037 796 Dihedral : 4.839 55.423 613 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.45 % Allowed : 6.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.35), residues: 550 helix: 1.69 (0.41), residues: 156 sheet: 1.10 (0.33), residues: 222 loop : -0.32 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.010 0.001 TYR A1135 PHE 0.009 0.001 PHE A 823 TRP 0.013 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4425) covalent geometry : angle 0.51738 ( 6021) SS BOND : bond 0.00456 ( 1) SS BOND : angle 0.62580 ( 2) hydrogen bonds : bond 0.03591 ( 286) hydrogen bonds : angle 4.98168 ( 819) *********************** 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 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7393 (tmt170) REVERT: A 632 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5978 (ttm170) REVERT: A 864 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 1064 MET cc_start: 0.7987 (tpt) cc_final: 0.7581 (tpp) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.0954 time to fit residues: 6.6237 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 2 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 = 0.3606 r_free = 0.3606 target = 0.127309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106508 restraints weight = 6654.749| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.03 r_work: 0.3231 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4426 Z= 0.159 Angle : 0.520 4.546 6023 Z= 0.284 Chirality : 0.041 0.143 629 Planarity : 0.004 0.038 796 Dihedral : 4.902 57.653 613 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.23 % Allowed : 7.80 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.35), residues: 550 helix: 1.71 (0.41), residues: 156 sheet: 1.10 (0.32), residues: 218 loop : -0.49 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.010 0.001 TYR A 801 PHE 0.008 0.001 PHE A 925 TRP 0.009 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4425) covalent geometry : angle 0.51977 ( 6021) SS BOND : bond 0.00460 ( 1) SS BOND : angle 0.47936 ( 2) hydrogen bonds : bond 0.03509 ( 286) hydrogen bonds : angle 4.94647 ( 819) *********************** 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: 10 poor density : 46 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7402 (tmt170) REVERT: A 632 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5925 (ttm170) REVERT: A 864 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 1064 MET cc_start: 0.8016 (tpt) cc_final: 0.7613 (tpp) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.0945 time to fit residues: 6.4303 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 : 0.198 ------------------------------------------------------------------------------- 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 1031 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105221 restraints weight = 6741.267| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.09 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1967 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= 0.186 Angle : 0.537 4.499 6023 Z= 0.294 Chirality : 0.041 0.142 629 Planarity : 0.004 0.037 796 Dihedral : 5.009 59.202 613 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.67 % Allowed : 8.69 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.35), residues: 550 helix: 1.62 (0.41), residues: 156 sheet: 1.01 (0.32), residues: 219 loop : -0.69 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 874 TYR 0.011 0.001 TYR A1135 PHE 0.008 0.001 PHE A 823 TRP 0.010 0.001 TRP A1056 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 4425) covalent geometry : angle 0.53723 ( 6021) SS BOND : bond 0.00556 ( 1) SS BOND : angle 0.53926 ( 2) hydrogen bonds : bond 0.03676 ( 286) hydrogen bonds : angle 4.98242 ( 819) *********************** 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 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 864 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 1064 MET cc_start: 0.8018 (tpt) cc_final: 0.7604 (tpp) outliers start: 12 outliers final: 10 residues processed: 54 average time/residue: 0.0764 time to fit residues: 5.2391 Evaluate side-chains 51 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.124120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102881 restraints weight = 6805.608| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.11 r_work: 0.3174 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4426 Z= 0.201 Angle : 0.554 4.857 6023 Z= 0.303 Chirality : 0.041 0.143 629 Planarity : 0.004 0.037 796 Dihedral : 5.066 59.721 613 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.67 % Allowed : 10.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.35), residues: 550 helix: 1.55 (0.41), residues: 156 sheet: 0.93 (0.33), residues: 218 loop : -0.78 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 874 TYR 0.011 0.001 TYR A1135 PHE 0.007 0.001 PHE A 823 TRP 0.010 0.001 TRP A 939 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4425) covalent geometry : angle 0.55396 ( 6021) SS BOND : bond 0.00557 ( 1) SS BOND : angle 0.54823 ( 2) hydrogen bonds : bond 0.03739 ( 286) hydrogen bonds : angle 4.97044 ( 819) *********************** 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 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 864 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 1064 MET cc_start: 0.8016 (tpt) cc_final: 0.7586 (tpp) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.0867 time to fit residues: 5.5803 Evaluate side-chains 49 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 3 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 = 0.125821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104461 restraints weight = 6696.479| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.10 r_work: 0.3202 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2127 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= 0.129 Angle : 0.503 4.737 6023 Z= 0.277 Chirality : 0.040 0.147 629 Planarity : 0.004 0.036 796 Dihedral : 4.916 59.531 613 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.35), residues: 550 helix: 1.68 (0.41), residues: 156 sheet: 1.03 (0.33), residues: 217 loop : -0.75 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 874 TYR 0.008 0.001 TYR A1135 PHE 0.006 0.001 PHE A 823 TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4425) covalent geometry : angle 0.50283 ( 6021) SS BOND : bond 0.00367 ( 1) SS BOND : angle 0.42440 ( 2) hydrogen bonds : bond 0.03252 ( 286) hydrogen bonds : angle 4.83144 ( 819) *********************** 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 : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7448 (tmt170) REVERT: A 660 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7355 (tt) REVERT: A 864 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8065 (t0) REVERT: A 1064 MET cc_start: 0.8009 (tpt) cc_final: 0.7563 (tpp) outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 0.0941 time to fit residues: 6.1185 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 : 0.170 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.0050 chunk 30 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 overall best weight: 0.2804 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.127550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106302 restraints weight = 6577.941| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.05 r_work: 0.3244 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4426 Z= 0.094 Angle : 0.476 5.774 6023 Z= 0.262 Chirality : 0.039 0.146 629 Planarity : 0.004 0.034 796 Dihedral : 4.721 58.939 613 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 11.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.36), residues: 550 helix: 1.87 (0.41), residues: 156 sheet: 1.12 (0.33), residues: 217 loop : -0.65 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 874 TYR 0.006 0.001 TYR A1132 PHE 0.006 0.001 PHE A 823 TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 4425) covalent geometry : angle 0.47555 ( 6021) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.28942 ( 2) hydrogen bonds : bond 0.02856 ( 286) hydrogen bonds : angle 4.69927 ( 819) *********************** 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 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8378 (tpp80) cc_final: 0.7447 (tmt170) REVERT: A 645 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 864 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8050 (t0) REVERT: A 1038 MET cc_start: 0.8160 (tmm) cc_final: 0.7797 (tmm) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.0926 time to fit residues: 6.7386 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105909 restraints weight = 6725.137| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.10 r_work: 0.3217 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4426 Z= 0.128 Angle : 0.510 6.390 6023 Z= 0.280 Chirality : 0.040 0.143 629 Planarity : 0.004 0.039 796 Dihedral : 4.762 58.899 613 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 11.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.36), residues: 550 helix: 1.87 (0.41), residues: 156 sheet: 1.10 (0.33), residues: 217 loop : -0.66 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 874 TYR 0.008 0.001 TYR A1135 PHE 0.010 0.001 PHE A 823 TRP 0.007 0.001 TRP A 873 HIS 0.002 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4425) covalent geometry : angle 0.51005 ( 6021) SS BOND : bond 0.00351 ( 1) SS BOND : angle 0.39968 ( 2) hydrogen bonds : bond 0.03068 ( 286) hydrogen bonds : angle 4.68933 ( 819) *********************** 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 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8320 (tpp80) cc_final: 0.7442 (tmt170) REVERT: A 660 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7388 (tt) REVERT: A 864 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 1038 MET cc_start: 0.8216 (tmm) cc_final: 0.7866 (tmm) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0912 time to fit residues: 6.1680 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 53 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.126725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105419 restraints weight = 6567.596| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.04 r_work: 0.3226 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4426 Z= 0.118 Angle : 0.506 6.210 6023 Z= 0.278 Chirality : 0.039 0.144 629 Planarity : 0.004 0.041 796 Dihedral : 4.746 58.442 613 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 11.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.36), residues: 550 helix: 1.86 (0.41), residues: 156 sheet: 1.12 (0.33), residues: 217 loop : -0.65 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 874 TYR 0.017 0.001 TYR A 619 PHE 0.010 0.001 PHE A 823 TRP 0.007 0.001 TRP A 873 HIS 0.002 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4425) covalent geometry : angle 0.50559 ( 6021) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.38037 ( 2) hydrogen bonds : bond 0.03008 ( 286) hydrogen bonds : angle 4.68034 ( 819) ********************** 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 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7440 (tmt170) REVERT: A 619 TYR cc_start: 0.7791 (t80) cc_final: 0.7587 (t80) REVERT: A 645 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 660 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7363 (tt) REVERT: A 864 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8043 (t0) REVERT: A 1038 MET cc_start: 0.8181 (tmm) cc_final: 0.7827 (tmm) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.0902 time to fit residues: 5.9545 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 : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104405 restraints weight = 6676.728| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- 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 0.035 4426 Z= 0.151 Angle : 0.526 5.884 6023 Z= 0.288 Chirality : 0.040 0.143 629 Planarity : 0.004 0.042 796 Dihedral : 4.839 58.442 613 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.36), residues: 550 helix: 1.76 (0.41), residues: 156 sheet: 1.06 (0.33), residues: 217 loop : -0.73 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 874 TYR 0.015 0.001 TYR A 619 PHE 0.010 0.001 PHE A 823 TRP 0.008 0.001 TRP A 939 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4425) covalent geometry : angle 0.52615 ( 6021) SS BOND : bond 0.00445 ( 1) SS BOND : angle 0.46330 ( 2) hydrogen bonds : bond 0.03283 ( 286) hydrogen bonds : angle 4.74185 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.08 seconds wall clock time: 22 minutes 13.26 seconds (1333.26 seconds total)