Starting phenix.real_space_refine on Sat May 10 02:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8h_44345/05_2025/9b8h_44345.cif" } resolution = 3.8 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= 0.031 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 16 5.16 5 C 2868 2.51 5 N 821 2.21 5 O 925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4630 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4585 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 562} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'BGC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.94, per 1000 atoms: 0.85 Number of scatterers: 4630 At special positions: 0 Unit cell: (70.2, 59.4, 128.52, 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 16 16.00 O 925 8.00 N 821 7.00 C 2868 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 Links applied BETA1-4 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 554.3 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 32.9% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 588 through 597 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 619 through 632 removed outlier: 4.240A pdb=" N ARG A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 670 through 684 removed outlier: 3.867A pdb=" N GLN A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 704 removed outlier: 4.552A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Proline residue: A 699 - end of helix removed outlier: 3.506A pdb=" N SER A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 704 " --> pdb=" O GLN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 725 removed outlier: 3.705A pdb=" N ALA A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.831A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 758 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1153 through 1157 Processing sheet with id=AA1, first strand: chain 'A' and resid 785 through 795 removed outlier: 6.464A pdb=" N GLN A 862 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 869 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N VAL A 894 " --> pdb=" O PRO A 917 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 907 through 917 current: chain 'A' and resid 938 through 953 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 961 through 968 current: chain 'A' and resid 997 through 1008 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1029 through 1037 current: chain 'A' and resid 1046 through 1060 removed outlier: 3.563A pdb=" N ARG A1099 " --> pdb=" O GLY A1051 " (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 230 hydrogen bonds defined for protein. 666 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: 1.33 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1570 1.35 - 1.46: 1116 1.46 - 1.58: 2022 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 4738 Sorted by residual: bond pdb=" C5 BGC B 2 " pdb=" O5 BGC B 2 " ideal model delta sigma weight residual 1.411 1.547 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C5 BGC B 2 " pdb=" C6 BGC B 2 " ideal model delta sigma weight residual 1.514 1.387 0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C5 BGC B 4 " pdb=" O5 BGC B 4 " ideal model delta sigma weight residual 1.411 1.537 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C5 BGC B 1 " pdb=" O5 BGC B 1 " ideal model delta sigma weight residual 1.411 1.528 -0.117 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C5 BGC B 4 " pdb=" C6 BGC B 4 " ideal model delta sigma weight residual 1.514 1.411 0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 4733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6091 1.40 - 2.79: 273 2.79 - 4.19: 63 4.19 - 5.58: 14 5.58 - 6.98: 3 Bond angle restraints: 6444 Sorted by residual: angle pdb=" CA ASP A 783 " pdb=" CB ASP A 783 " pdb=" CG ASP A 783 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CA THR A1107 " pdb=" C THR A1107 " pdb=" N SER A1108 " ideal model delta sigma weight residual 115.54 120.62 -5.08 1.52e+00 4.33e-01 1.12e+01 angle pdb=" CA ARG A 617 " pdb=" CB ARG A 617 " pdb=" CG ARG A 617 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" N ALA A 689 " pdb=" CA ALA A 689 " pdb=" C ALA A 689 " ideal model delta sigma weight residual 113.88 109.92 3.96 1.23e+00 6.61e-01 1.04e+01 angle pdb=" CA THR A 885 " pdb=" CB THR A 885 " pdb=" OG1 THR A 885 " ideal model delta sigma weight residual 109.60 104.82 4.78 1.50e+00 4.44e-01 1.01e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 2518 15.98 - 31.95: 241 31.95 - 47.93: 68 47.93 - 63.90: 17 63.90 - 79.88: 4 Dihedral angle restraints: 2848 sinusoidal: 1166 harmonic: 1682 Sorted by residual: dihedral pdb=" CA SER A 670 " pdb=" C SER A 670 " pdb=" N LEU A 671 " pdb=" CA LEU A 671 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LYS A 955 " pdb=" C LYS A 955 " pdb=" N GLY A 956 " pdb=" CA GLY A 956 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN A 668 " pdb=" C ASN A 668 " pdb=" N ALA A 669 " pdb=" CA ALA A 669 " ideal model delta harmonic sigma weight residual 180.00 163.92 16.08 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 526 0.043 - 0.085: 100 0.085 - 0.128: 43 0.128 - 0.170: 15 0.170 - 0.213: 3 Chirality restraints: 687 Sorted by residual: chirality pdb=" C1 BGC B 4 " pdb=" O4 BGC B 3 " pdb=" C2 BGC B 4 " pdb=" O5 BGC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.67e+00 chirality pdb=" C1 BGC B 2 " pdb=" O4 BGC B 1 " pdb=" C2 BGC B 2 " pdb=" O5 BGC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.31e+00 chirality pdb=" C1 BGC B 3 " pdb=" O4 BGC B 2 " pdb=" C2 BGC B 3 " pdb=" O5 BGC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.57e+00 ... (remaining 684 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1104 " 0.254 9.50e-02 1.11e+02 1.14e-01 7.99e+00 pdb=" NE ARG A1104 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A1104 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1104 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1104 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 769 " -0.170 9.50e-02 1.11e+02 7.64e-02 3.63e+00 pdb=" NE ARG A 769 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 769 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 769 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 769 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1042 " -0.155 9.50e-02 1.11e+02 6.97e-02 3.01e+00 pdb=" NE ARG A1042 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A1042 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A1042 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1042 " -0.005 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1587 2.84 - 3.35: 4222 3.35 - 3.87: 7661 3.87 - 4.38: 8455 4.38 - 4.90: 15120 Nonbonded interactions: 37045 Sorted by model distance: nonbonded pdb=" O THR A 755 " pdb=" OG1 THR A 758 " model vdw 2.324 3.040 nonbonded pdb=" O THR A 910 " pdb=" OG1 THR A 910 " model vdw 2.361 3.040 nonbonded pdb=" O LEU A 641 " pdb=" OG1 THR A 644 " model vdw 2.397 3.040 nonbonded pdb=" O SER A 586 " pdb=" OE1 GLU A 589 " model vdw 2.402 3.040 nonbonded pdb=" O GLN A 575 " pdb=" OG1 THR A 579 " model vdw 2.403 3.040 ... (remaining 37040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.007 0.136 4742 Z= 0.396 Angle : 0.692 6.977 6455 Z= 0.417 Chirality : 0.047 0.213 687 Planarity : 0.006 0.114 848 Dihedral : 14.218 79.880 1773 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.42 % Allowed : 17.40 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.71 (0.36), residues: 585 helix: 1.25 (0.38), residues: 186 sheet: 0.75 (0.35), residues: 215 loop : -0.58 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 612 HIS 0.002 0.000 HIS A1058 PHE 0.012 0.001 PHE A 694 TYR 0.011 0.001 TYR A 988 ARG 0.004 0.000 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.02859 ( 3) link_BETA1-4 : angle 2.97477 ( 9) hydrogen bonds : bond 0.18962 ( 230) hydrogen bonds : angle 8.00062 ( 666) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.18914 ( 2) covalent geometry : bond 0.00708 ( 4738) covalent geometry : angle 0.68338 ( 6444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.505 Fit side-chains REVERT: A 1048 TRP cc_start: 0.8428 (p90) cc_final: 0.8196 (p90) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.2031 time to fit residues: 13.4830 Evaluate side-chains 44 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.121907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098102 restraints weight = 8222.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100744 restraints weight = 4442.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102429 restraints weight = 2890.594| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4742 Z= 0.133 Angle : 0.551 6.111 6455 Z= 0.287 Chirality : 0.039 0.146 687 Planarity : 0.004 0.036 848 Dihedral : 4.111 21.426 730 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.52 % Allowed : 16.77 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.84 (0.36), residues: 585 helix: 1.55 (0.39), residues: 186 sheet: 0.65 (0.35), residues: 217 loop : -0.49 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 939 HIS 0.005 0.001 HIS A1009 PHE 0.013 0.002 PHE A 754 TYR 0.010 0.001 TYR A1010 ARG 0.004 0.001 ARG A 772 Details of bonding type rmsd link_BETA1-4 : bond 0.00346 ( 3) link_BETA1-4 : angle 1.52925 ( 9) hydrogen bonds : bond 0.03138 ( 230) hydrogen bonds : angle 5.64400 ( 666) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.30081 ( 2) covalent geometry : bond 0.00294 ( 4738) covalent geometry : angle 0.54865 ( 6444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.460 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 0.1591 time to fit residues: 12.1278 Evaluate side-chains 48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1070 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 862 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094958 restraints weight = 8389.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097612 restraints weight = 4634.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099343 restraints weight = 3024.622| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4742 Z= 0.129 Angle : 0.521 5.731 6455 Z= 0.272 Chirality : 0.039 0.141 687 Planarity : 0.004 0.028 848 Dihedral : 4.022 22.282 730 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.73 % Allowed : 17.40 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.83 (0.36), residues: 585 helix: 1.59 (0.39), residues: 183 sheet: 0.57 (0.35), residues: 216 loop : -0.40 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 939 HIS 0.004 0.001 HIS A1009 PHE 0.015 0.002 PHE A 754 TYR 0.014 0.001 TYR A 987 ARG 0.005 0.000 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 1.51969 ( 9) hydrogen bonds : bond 0.03176 ( 230) hydrogen bonds : angle 5.28169 ( 666) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.25946 ( 2) covalent geometry : bond 0.00291 ( 4738) covalent geometry : angle 0.51847 ( 6444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.476 Fit side-chains REVERT: A 712 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6690 (mtm) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.1644 time to fit residues: 11.3665 Evaluate side-chains 47 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.117627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093435 restraints weight = 8588.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096076 restraints weight = 4722.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097807 restraints weight = 3069.230| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4742 Z= 0.149 Angle : 0.537 7.035 6455 Z= 0.278 Chirality : 0.039 0.134 687 Planarity : 0.004 0.050 848 Dihedral : 4.146 23.896 730 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.74 (0.36), residues: 585 helix: 1.44 (0.39), residues: 183 sheet: 0.59 (0.36), residues: 211 loop : -0.44 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 983 HIS 0.004 0.001 HIS A1009 PHE 0.009 0.001 PHE A1111 TYR 0.016 0.001 TYR A 987 ARG 0.013 0.001 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00387 ( 3) link_BETA1-4 : angle 1.53684 ( 9) hydrogen bonds : bond 0.02954 ( 230) hydrogen bonds : angle 5.20100 ( 666) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.21098 ( 2) covalent geometry : bond 0.00338 ( 4738) covalent geometry : angle 0.53471 ( 6444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.468 Fit side-chains REVERT: A 712 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6793 (mtm) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.1666 time to fit residues: 10.9781 Evaluate side-chains 50 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1145 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092073 restraints weight = 8674.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094731 restraints weight = 4702.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096478 restraints weight = 3051.197| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4742 Z= 0.157 Angle : 0.529 6.280 6455 Z= 0.275 Chirality : 0.039 0.131 687 Planarity : 0.004 0.058 848 Dihedral : 4.250 23.762 730 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.73 % Allowed : 18.24 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.73 (0.36), residues: 585 helix: 1.39 (0.39), residues: 183 sheet: 0.67 (0.36), residues: 210 loop : -0.52 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 983 HIS 0.003 0.001 HIS A1009 PHE 0.010 0.002 PHE A1111 TYR 0.016 0.002 TYR A 987 ARG 0.010 0.001 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00348 ( 3) link_BETA1-4 : angle 1.58115 ( 9) hydrogen bonds : bond 0.02983 ( 230) hydrogen bonds : angle 5.14911 ( 666) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.39680 ( 2) covalent geometry : bond 0.00355 ( 4738) covalent geometry : angle 0.52592 ( 6444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6865 (mtm) outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.1761 time to fit residues: 11.6143 Evaluate side-chains 51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1145 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.0040 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.116825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092324 restraints weight = 8608.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095121 restraints weight = 4513.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096947 restraints weight = 2870.926| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4742 Z= 0.115 Angle : 0.512 6.091 6455 Z= 0.265 Chirality : 0.038 0.134 687 Planarity : 0.004 0.047 848 Dihedral : 4.123 23.880 730 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.35 % Allowed : 18.45 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.79 (0.36), residues: 585 helix: 1.49 (0.38), residues: 183 sheet: 0.67 (0.36), residues: 211 loop : -0.49 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1046 HIS 0.002 0.001 HIS A1058 PHE 0.008 0.001 PHE A1111 TYR 0.016 0.001 TYR A 987 ARG 0.010 0.000 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 1.42306 ( 9) hydrogen bonds : bond 0.02714 ( 230) hydrogen bonds : angle 5.03438 ( 666) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.12344 ( 2) covalent geometry : bond 0.00261 ( 4738) covalent geometry : angle 0.50948 ( 6444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6759 (mtm) REVERT: A 1102 LEU cc_start: 0.8552 (tp) cc_final: 0.8241 (tp) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1678 time to fit residues: 11.4750 Evaluate side-chains 50 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1143 ASP Chi-restraints excluded: chain A residue 1145 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.116581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092009 restraints weight = 8618.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094767 restraints weight = 4537.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096602 restraints weight = 2899.330| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4742 Z= 0.128 Angle : 0.523 6.251 6455 Z= 0.270 Chirality : 0.038 0.133 687 Planarity : 0.004 0.047 848 Dihedral : 4.142 22.680 730 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.35 % Allowed : 19.08 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.78 (0.36), residues: 585 helix: 1.51 (0.38), residues: 183 sheet: 0.64 (0.36), residues: 211 loop : -0.51 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 939 HIS 0.002 0.001 HIS A1009 PHE 0.008 0.001 PHE A1111 TYR 0.018 0.001 TYR A 987 ARG 0.009 0.000 ARG A1099 Details of bonding type rmsd link_BETA1-4 : bond 0.00364 ( 3) link_BETA1-4 : angle 1.47404 ( 9) hydrogen bonds : bond 0.02782 ( 230) hydrogen bonds : angle 5.01514 ( 666) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.17068 ( 2) covalent geometry : bond 0.00292 ( 4738) covalent geometry : angle 0.52101 ( 6444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6824 (mtm) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.1684 time to fit residues: 11.5440 Evaluate side-chains 50 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1145 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090597 restraints weight = 8685.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093342 restraints weight = 4608.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095146 restraints weight = 2961.343| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4742 Z= 0.160 Angle : 0.551 8.102 6455 Z= 0.286 Chirality : 0.039 0.132 687 Planarity : 0.004 0.070 848 Dihedral : 4.309 22.348 730 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.94 % Allowed : 20.55 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.74 (0.36), residues: 585 helix: 1.57 (0.38), residues: 180 sheet: 0.61 (0.36), residues: 209 loop : -0.57 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 939 HIS 0.003 0.001 HIS A1009 PHE 0.010 0.002 PHE A1111 TYR 0.018 0.001 TYR A 987 ARG 0.010 0.001 ARG A1099 Details of bonding type rmsd link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 1.61619 ( 9) hydrogen bonds : bond 0.02924 ( 230) hydrogen bonds : angle 5.07694 ( 666) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.15931 ( 2) covalent geometry : bond 0.00364 ( 4738) covalent geometry : angle 0.54853 ( 6444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.489 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 44 average time/residue: 0.1956 time to fit residues: 11.2996 Evaluate side-chains 45 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 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 = 0.3562 r_free = 0.3562 target = 0.113530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089360 restraints weight = 8714.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092046 restraints weight = 4635.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093804 restraints weight = 2984.450| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4742 Z= 0.194 Angle : 0.578 8.237 6455 Z= 0.300 Chirality : 0.040 0.132 687 Planarity : 0.004 0.056 848 Dihedral : 4.487 22.139 730 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.73 % Allowed : 20.55 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.55 (0.36), residues: 585 helix: 1.34 (0.38), residues: 182 sheet: 0.49 (0.36), residues: 209 loop : -0.59 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 793 HIS 0.003 0.001 HIS A1009 PHE 0.012 0.002 PHE A1111 TYR 0.020 0.002 TYR A 987 ARG 0.008 0.001 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00340 ( 3) link_BETA1-4 : angle 1.82709 ( 9) hydrogen bonds : bond 0.03157 ( 230) hydrogen bonds : angle 5.18825 ( 666) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.13635 ( 2) covalent geometry : bond 0.00440 ( 4738) covalent geometry : angle 0.57453 ( 6444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.6871 (m-80) cc_final: 0.6537 (m-80) outliers start: 13 outliers final: 12 residues processed: 44 average time/residue: 0.1626 time to fit residues: 9.5754 Evaluate side-chains 45 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.115229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091709 restraints weight = 8522.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094330 restraints weight = 4541.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096022 restraints weight = 2931.075| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4742 Z= 0.123 Angle : 0.562 8.813 6455 Z= 0.286 Chirality : 0.039 0.138 687 Planarity : 0.004 0.058 848 Dihedral : 4.367 21.301 730 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.31 % Allowed : 21.38 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.56 (0.36), residues: 585 helix: 1.32 (0.38), residues: 182 sheet: 0.54 (0.36), residues: 210 loop : -0.63 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1058 PHE 0.009 0.001 PHE A1111 TYR 0.020 0.001 TYR A 987 ARG 0.008 0.000 ARG A 617 Details of bonding type rmsd link_BETA1-4 : bond 0.00312 ( 3) link_BETA1-4 : angle 1.60077 ( 9) hydrogen bonds : bond 0.02844 ( 230) hydrogen bonds : angle 5.05106 ( 666) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.04199 ( 2) covalent geometry : bond 0.00281 ( 4738) covalent geometry : angle 0.55887 ( 6444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.515 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 42 average time/residue: 0.1578 time to fit residues: 8.9887 Evaluate side-chains 45 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 13 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.115516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091325 restraints weight = 8582.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094088 restraints weight = 4503.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095833 restraints weight = 2869.997| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4742 Z= 0.125 Angle : 0.551 9.687 6455 Z= 0.280 Chirality : 0.039 0.135 687 Planarity : 0.004 0.065 848 Dihedral : 4.277 20.553 730 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.31 % Allowed : 21.38 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.55 (0.36), residues: 585 helix: 1.31 (0.38), residues: 182 sheet: 0.53 (0.36), residues: 210 loop : -0.63 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.002 0.001 HIS A1058 PHE 0.009 0.001 PHE A1111 TYR 0.021 0.001 TYR A 987 ARG 0.004 0.000 ARG A1099 Details of bonding type rmsd link_BETA1-4 : bond 0.00302 ( 3) link_BETA1-4 : angle 1.56939 ( 9) hydrogen bonds : bond 0.02784 ( 230) hydrogen bonds : angle 4.96528 ( 666) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.10956 ( 2) covalent geometry : bond 0.00288 ( 4738) covalent geometry : angle 0.54838 ( 6444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.67 seconds wall clock time: 31 minutes 52.48 seconds (1912.48 seconds total)