Starting phenix.real_space_refine on Thu Mar 6 03:29:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8h_44345/03_2025/9b8h_44345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8h_44345/03_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_44345/03_2025/9b8h_44345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8h_44345/03_2025/9b8h_44345.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8h_44345/03_2025/9b8h_44345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8h_44345/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.42, per 1000 atoms: 0.74 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: 1.29 Conformation dependent library (CDL) restraints added in 572.2 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: 0.52 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: 1.39 Time building geometry restraints manager: 1.41 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: 1.930 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: 15.700 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- 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 4738 Z= 0.469 Angle : 0.683 6.977 6444 Z= 0.416 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 *********************** 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 : 0.495 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: 0.2059 time to fit residues: 13.6086 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 : 0.461 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098093 restraints weight = 8222.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100721 restraints weight = 4450.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102468 restraints weight = 2897.023| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- 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 4738 Z= 0.192 Angle : 0.549 6.111 6444 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 *********************** 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 : 0.511 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 0.1606 time to fit residues: 12.3629 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 : 0.480 ------------------------------------------------------------------------------- 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: 0.1980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.119053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094979 restraints weight = 8391.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097619 restraints weight = 4579.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099320 restraints weight = 2997.558| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4738 Z= 0.195 Angle : 0.519 5.706 6444 Z= 0.272 Chirality : 0.039 0.142 687 Planarity : 0.004 0.029 848 Dihedral : 4.021 22.204 730 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % 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: 0.56 (0.35), residues: 216 loop : -0.41 (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 0.014 0.002 PHE A 754 TYR 0.014 0.001 TYR A 987 ARG 0.004 0.000 ARG A 617 *********************** 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 : 0.481 Fit side-chains REVERT: A 712 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6694 (mtm) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.1641 time to fit residues: 11.4472 Evaluate side-chains 48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 9.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.116952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092576 restraints weight = 8632.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095238 restraints weight = 4707.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096918 restraints weight = 3068.184| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4738 Z= 0.254 Angle : 0.548 6.912 6444 Z= 0.285 Chirality : 0.039 0.135 687 Planarity : 0.004 0.058 848 Dihedral : 4.223 24.038 730 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.94 % Allowed : 18.24 % Favored : 78.83 % 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: 1.39 (0.39), residues: 183 sheet: 0.61 (0.36), residues: 210 loop : -0.47 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 983 HIS 0.004 0.001 HIS A1009 PHE 0.009 0.002 PHE A 836 TYR 0.014 0.002 TYR A 987 ARG 0.010 0.001 ARG A 617 *********************** 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: 14 poor density : 41 time to evaluate : 0.520 Fit side-chains REVERT: A 712 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6768 (mtm) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.1550 time to fit residues: 10.3127 Evaluate side-chains 51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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: 0.0070 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.117967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093655 restraints weight = 8621.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096364 restraints weight = 4640.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098139 restraints weight = 3005.409| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4738 Z= 0.168 Angle : 0.504 6.291 6444 Z= 0.262 Chirality : 0.038 0.134 687 Planarity : 0.004 0.048 848 Dihedral : 4.094 24.078 730 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.31 % Allowed : 18.24 % Favored : 79.45 % 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: 0.82 (0.36), residues: 585 helix: 1.50 (0.39), residues: 183 sheet: 0.65 (0.36), residues: 212 loop : -0.42 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 793 HIS 0.002 0.001 HIS A1009 PHE 0.009 0.001 PHE A1111 TYR 0.016 0.001 TYR A 987 ARG 0.009 0.001 ARG A 617 *********************** 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 50 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6790 (mtm) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.1516 time to fit residues: 9.4514 Evaluate side-chains 47 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 894 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: 0.4980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095229 restraints weight = 8493.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097899 restraints weight = 4577.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099689 restraints weight = 2969.170| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 4738 Z= 0.128 Angle : 0.492 6.233 6444 Z= 0.255 Chirality : 0.037 0.135 687 Planarity : 0.004 0.041 848 Dihedral : 3.952 23.976 730 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % 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: 0.96 (0.36), residues: 585 helix: 1.64 (0.39), residues: 183 sheet: 0.74 (0.36), residues: 216 loop : -0.39 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 793 HIS 0.002 0.001 HIS A1058 PHE 0.007 0.001 PHE A1111 TYR 0.017 0.001 TYR A 987 ARG 0.004 0.000 ARG A 617 *********************** 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: 13 poor density : 45 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6524 (mtm) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 0.1482 time to fit residues: 10.8676 Evaluate side-chains 47 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 813 VAL Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1143 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.116627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091832 restraints weight = 8616.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.094568 restraints weight = 4601.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096420 restraints weight = 2943.505| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 0.051 4738 Z= 0.204 Angle : 0.529 7.721 6444 Z= 0.271 Chirality : 0.039 0.132 687 Planarity : 0.004 0.042 848 Dihedral : 4.081 22.555 730 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.73 % Allowed : 19.08 % 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: 0.82 (0.36), residues: 585 helix: 1.61 (0.39), residues: 183 sheet: 0.68 (0.36), residues: 206 loop : -0.56 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 939 HIS 0.002 0.001 HIS A1009 PHE 0.008 0.001 PHE A 836 TYR 0.018 0.001 TYR A 987 ARG 0.005 0.000 ARG A 617 *********************** 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 54 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.524 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.1490 time to fit residues: 10.1168 Evaluate side-chains 49 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 1143 ASP 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: 0.6980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.115349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090558 restraints weight = 8710.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093288 restraints weight = 4627.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095113 restraints weight = 2979.805| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4738 Z= 0.242 Angle : 0.554 8.380 6444 Z= 0.289 Chirality : 0.039 0.133 687 Planarity : 0.004 0.030 848 Dihedral : 4.275 22.020 730 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.94 % Allowed : 19.29 % Favored : 77.78 % 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: 1.49 (0.38), residues: 183 sheet: 0.65 (0.36), residues: 209 loop : -0.49 (0.48), residues: 193 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 0.019 0.001 TYR A 987 ARG 0.007 0.000 ARG A 617 *********************** 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 52 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6855 (mtm) outliers start: 14 outliers final: 12 residues processed: 46 average time/residue: 0.1578 time to fit residues: 9.8185 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 : 0.516 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091151 restraints weight = 8650.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093882 restraints weight = 4595.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095670 restraints weight = 2953.072| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4738 Z= 0.211 Angle : 0.547 7.977 6444 Z= 0.285 Chirality : 0.039 0.134 687 Planarity : 0.004 0.032 848 Dihedral : 4.261 21.146 730 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.14 % Allowed : 19.92 % Favored : 76.94 % 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: 0.65 (0.36), residues: 585 helix: 1.35 (0.38), residues: 183 sheet: 0.61 (0.36), residues: 209 loop : -0.56 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 939 HIS 0.002 0.001 HIS A1009 PHE 0.009 0.001 PHE A1111 TYR 0.020 0.001 TYR A 987 ARG 0.009 0.000 ARG A 617 *********************** 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 49 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 712 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6855 (mtm) outliers start: 15 outliers final: 12 residues processed: 44 average time/residue: 0.1624 time to fit residues: 9.6532 Evaluate side-chains 46 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.115653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.091236 restraints weight = 8580.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093984 restraints weight = 4568.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095754 restraints weight = 2917.967| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4738 Z= 0.210 Angle : 0.544 7.764 6444 Z= 0.284 Chirality : 0.039 0.133 687 Planarity : 0.004 0.032 848 Dihedral : 4.245 21.056 730 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: 0.63 (0.36), residues: 585 helix: 1.35 (0.38), residues: 182 sheet: 0.55 (0.36), residues: 209 loop : -0.52 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 983 HIS 0.002 0.001 HIS A1009 PHE 0.010 0.001 PHE A1111 TYR 0.020 0.001 TYR A 987 ARG 0.008 0.000 ARG A 617 ********************** 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 49 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 647 ASP cc_start: 0.7915 (m-30) cc_final: 0.7176 (t0) REVERT: A 712 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6834 (mtm) outliers start: 13 outliers final: 12 residues processed: 45 average time/residue: 0.1707 time to fit residues: 10.2581 Evaluate side-chains 47 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- 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 = 0.114950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090553 restraints weight = 8640.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093285 restraints weight = 4609.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095079 restraints weight = 2953.090| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4738 Z= 0.228 Angle : 0.551 7.546 6444 Z= 0.287 Chirality : 0.039 0.133 687 Planarity : 0.004 0.032 848 Dihedral : 4.298 20.902 730 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.73 % Allowed : 20.96 % 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: 0.58 (0.36), residues: 585 helix: 1.28 (0.38), residues: 182 sheet: 0.54 (0.36), residues: 209 loop : -0.54 (0.48), residues: 194 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 0.001 PHE A1111 TYR 0.020 0.001 TYR A 987 ARG 0.007 0.000 ARG A 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.03 seconds wall clock time: 31 minutes 6.37 seconds (1866.37 seconds total)