Starting phenix.real_space_refine on Fri Dec 27 04:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta6_41130/12_2024/8ta6_41130.cif" } resolution = 4.03 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= 0.000 sd= 0.051 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 10 5.16 5 C 1368 2.51 5 N 400 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2158 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "B" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Time building chain proxies: 2.54, per 1000 atoms: 1.18 Number of scatterers: 2158 At special positions: 0 Unit cell: (75.68, 70.004, 80.41, 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 10 16.00 O 380 8.00 N 400 7.00 C 1368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 273.1 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 4 sheets defined 36.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.648A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 802 through 811 removed outlier: 4.575A pdb=" N THR A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.795A pdb=" N ALA B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 599 through 604' Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.570A pdb=" N VAL B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 814 removed outlier: 3.513A pdb=" N THR B 806 " --> pdb=" O SER B 802 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 813 " --> pdb=" O ILE B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 839 Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.330A pdb=" N VAL A 591 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 612 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER A 626 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 614 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 796 through 798 removed outlier: 5.908A pdb=" N LEU A 797 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 828 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 822 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 590 through 592 removed outlier: 6.736A pdb=" N VAL B 591 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 625 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 796 through 797 removed outlier: 3.840A pdb=" N GLY B 828 " --> pdb=" O VAL B 820 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 640 1.34 - 1.46: 283 1.46 - 1.58: 1253 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 2192 Sorted by residual: bond pdb=" CA ASP A 791 " pdb=" C ASP A 791 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.26e-02 6.30e+03 6.44e+00 bond pdb=" CZ ARG B 629 " pdb=" NH2 ARG B 629 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" CZ ARG A 629 " pdb=" NH2 ARG A 629 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.25e+00 bond pdb=" CD2 HIS A 804 " pdb=" NE2 HIS A 804 " ideal model delta sigma weight residual 1.374 1.401 -0.027 1.10e-02 8.26e+03 6.20e+00 bond pdb=" CZ ARG B 577 " pdb=" NH2 ARG B 577 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.17e+00 ... (remaining 2187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 1943 1.75 - 3.50: 777 3.50 - 5.24: 196 5.24 - 6.99: 37 6.99 - 8.74: 5 Bond angle restraints: 2958 Sorted by residual: angle pdb=" CA ASP A 787 " pdb=" CB ASP A 787 " pdb=" CG ASP A 787 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" C MET A 584 " pdb=" N VAL A 585 " pdb=" CA VAL A 585 " ideal model delta sigma weight residual 120.98 128.03 -7.05 1.36e+00 5.41e-01 2.69e+01 angle pdb=" N MET A 611 " pdb=" CA MET A 611 " pdb=" C MET A 611 " ideal model delta sigma weight residual 108.99 116.66 -7.67 1.57e+00 4.06e-01 2.39e+01 angle pdb=" OE1 GLN B 639 " pdb=" CD GLN B 639 " pdb=" NE2 GLN B 639 " ideal model delta sigma weight residual 122.60 117.77 4.83 1.00e+00 1.00e+00 2.34e+01 angle pdb=" N GLY B 571 " pdb=" CA GLY B 571 " pdb=" C GLY B 571 " ideal model delta sigma weight residual 111.21 116.18 -4.97 1.04e+00 9.25e-01 2.28e+01 ... (remaining 2953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1196 17.58 - 35.16: 116 35.16 - 52.74: 17 52.74 - 70.31: 5 70.31 - 87.89: 4 Dihedral angle restraints: 1338 sinusoidal: 552 harmonic: 786 Sorted by residual: dihedral pdb=" CA ARG A 572 " pdb=" C ARG A 572 " pdb=" N HIS A 573 " pdb=" CA HIS A 573 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL B 585 " pdb=" C VAL B 585 " pdb=" N ARG B 586 " pdb=" CA ARG B 586 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ARG A 610 " pdb=" C ARG A 610 " pdb=" N MET A 611 " pdb=" CA MET A 611 " ideal model delta harmonic sigma weight residual 180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 1335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 174 0.072 - 0.143: 120 0.143 - 0.214: 46 0.214 - 0.285: 11 0.285 - 0.357: 1 Chirality restraints: 352 Sorted by residual: chirality pdb=" CA MET B 621 " pdb=" N MET B 621 " pdb=" C MET B 621 " pdb=" CB MET B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA GLN A 575 " pdb=" N GLN A 575 " pdb=" C GLN A 575 " pdb=" CB GLN A 575 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA MET A 621 " pdb=" N MET A 621 " pdb=" C MET A 621 " pdb=" CB MET A 621 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 349 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 785 " 0.125 2.00e-02 2.50e+03 7.65e-02 1.02e+02 pdb=" CG PHE A 785 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE A 785 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 PHE A 785 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 785 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 785 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 785 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 570 " 0.096 2.00e-02 2.50e+03 4.79e-02 5.72e+01 pdb=" CG TRP A 570 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 570 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 570 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 570 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 570 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 570 " -0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 570 " 0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 570 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 570 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 570 " 0.080 2.00e-02 2.50e+03 3.96e-02 3.91e+01 pdb=" CG TRP B 570 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 570 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 570 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP B 570 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP B 570 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 570 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 570 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 570 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 570 " 0.047 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 992 3.00 - 3.47: 2273 3.47 - 3.95: 3209 3.95 - 4.42: 3182 4.42 - 4.90: 5389 Nonbonded interactions: 15045 Sorted by model distance: nonbonded pdb=" OE2 GLU A 628 " pdb=" OG SER A 630 " model vdw 2.524 3.040 nonbonded pdb=" OE1 GLU B 616 " pdb=" OG SER B 620 " model vdw 2.543 3.040 nonbonded pdb=" OG SER A 617 " pdb=" OE2 GLU A 619 " model vdw 2.547 3.040 nonbonded pdb=" OG1 THR B 831 " pdb=" OE1 GLU B 834 " model vdw 2.560 3.040 nonbonded pdb=" N SER A 822 " pdb=" O SER A 822 " model vdw 2.579 2.496 ... (remaining 15040 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.900 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.013 0.039 2192 Z= 0.837 Angle : 1.987 8.737 2958 Z= 1.304 Chirality : 0.103 0.357 352 Planarity : 0.014 0.087 372 Dihedral : 15.103 87.892 826 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.40 % Favored : 90.23 % Rotamer: Outliers : 2.10 % Allowed : 15.13 % Favored : 82.77 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.49), residues: 266 helix: -2.32 (0.45), residues: 76 sheet: -2.24 (0.97), residues: 22 loop : -0.90 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.036 TRP A 570 HIS 0.006 0.002 HIS B 590 PHE 0.125 0.019 PHE A 785 TYR 0.052 0.021 TYR A 819 ARG 0.002 0.001 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 590 HIS cc_start: 0.9622 (p-80) cc_final: 0.9188 (p-80) REVERT: A 611 MET cc_start: 0.8216 (tpp) cc_final: 0.7962 (tpp) REVERT: A 836 ARG cc_start: 0.6537 (mmt180) cc_final: 0.5747 (mpt180) REVERT: B 577 ARG cc_start: 0.8577 (ttp80) cc_final: 0.7928 (mmt180) REVERT: B 581 GLU cc_start: 0.8586 (tt0) cc_final: 0.8386 (tt0) REVERT: B 582 ASP cc_start: 0.8170 (m-30) cc_final: 0.7785 (m-30) REVERT: B 607 THR cc_start: 0.9365 (p) cc_final: 0.8966 (p) REVERT: B 629 ARG cc_start: 0.7950 (mtt180) cc_final: 0.5543 (ptm160) REVERT: B 785 PHE cc_start: 0.8708 (p90) cc_final: 0.8475 (p90) REVERT: B 834 GLU cc_start: 0.9537 (mp0) cc_final: 0.9121 (mp0) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 0.2300 time to fit residues: 18.1970 Evaluate side-chains 49 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2192 Z= 0.192 Angle : 0.697 5.014 2958 Z= 0.372 Chirality : 0.046 0.139 352 Planarity : 0.005 0.042 372 Dihedral : 6.882 23.171 300 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.51), residues: 266 helix: -0.83 (0.57), residues: 73 sheet: -1.38 (0.82), residues: 40 loop : -0.83 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 570 HIS 0.004 0.001 HIS A 807 PHE 0.013 0.002 PHE A 810 TYR 0.006 0.001 TYR A 819 ARG 0.003 0.001 ARG A 825 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 ASP cc_start: 0.6783 (m-30) cc_final: 0.6530 (t0) REVERT: A 590 HIS cc_start: 0.9614 (p-80) cc_final: 0.9161 (p-80) REVERT: A 836 ARG cc_start: 0.5882 (mmt180) cc_final: 0.4428 (tmt170) REVERT: B 577 ARG cc_start: 0.8475 (ttp80) cc_final: 0.7898 (mmt180) REVERT: B 596 THR cc_start: 0.6434 (t) cc_final: 0.6203 (p) REVERT: B 607 THR cc_start: 0.9404 (p) cc_final: 0.9128 (p) REVERT: B 629 ARG cc_start: 0.7852 (mtt180) cc_final: 0.6790 (ttm170) REVERT: B 825 ARG cc_start: 0.7176 (tmt170) cc_final: 0.6971 (tmt170) REVERT: B 834 GLU cc_start: 0.9544 (mp0) cc_final: 0.9295 (mp0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2245 time to fit residues: 17.6089 Evaluate side-chains 49 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2192 Z= 0.161 Angle : 0.599 5.747 2958 Z= 0.318 Chirality : 0.043 0.130 352 Planarity : 0.004 0.044 372 Dihedral : 5.820 19.673 300 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.51), residues: 266 helix: -0.30 (0.59), residues: 80 sheet: -0.87 (1.03), residues: 25 loop : -1.23 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 570 HIS 0.003 0.001 HIS B 817 PHE 0.011 0.002 PHE A 810 TYR 0.007 0.001 TYR B 819 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.5858 (tpt) cc_final: 0.5347 (tpt) REVERT: A 590 HIS cc_start: 0.9623 (p-80) cc_final: 0.9158 (p-80) REVERT: A 784 ASN cc_start: 0.9310 (t0) cc_final: 0.9086 (t0) REVERT: A 825 ARG cc_start: 0.7549 (mmm160) cc_final: 0.7282 (mmm160) REVERT: A 836 ARG cc_start: 0.6250 (mmt180) cc_final: 0.4799 (tmt170) REVERT: B 577 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7873 (mpt90) REVERT: B 596 THR cc_start: 0.6583 (t) cc_final: 0.6318 (p) REVERT: B 607 THR cc_start: 0.9380 (p) cc_final: 0.9086 (p) REVERT: B 621 MET cc_start: 0.8251 (mtm) cc_final: 0.7975 (mpp) REVERT: B 629 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6128 (ttm-80) REVERT: B 834 GLU cc_start: 0.9539 (mp0) cc_final: 0.9289 (mp0) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2479 time to fit residues: 18.9987 Evaluate side-chains 48 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2192 Z= 0.153 Angle : 0.570 4.404 2958 Z= 0.299 Chirality : 0.043 0.156 352 Planarity : 0.004 0.040 372 Dihedral : 5.364 18.726 300 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.49), residues: 266 helix: -0.20 (0.59), residues: 80 sheet: -0.96 (0.94), residues: 25 loop : -1.19 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 570 HIS 0.003 0.001 HIS A 804 PHE 0.008 0.001 PHE A 810 TYR 0.009 0.001 TYR B 819 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 VAL cc_start: 0.9275 (p) cc_final: 0.9024 (p) REVERT: A 584 MET cc_start: 0.5854 (tpt) cc_final: 0.5488 (tpt) REVERT: A 590 HIS cc_start: 0.9589 (p-80) cc_final: 0.9138 (p-80) REVERT: A 621 MET cc_start: 0.7704 (ptp) cc_final: 0.7358 (ptp) REVERT: A 784 ASN cc_start: 0.9332 (t0) cc_final: 0.9121 (t0) REVERT: A 836 ARG cc_start: 0.6200 (mmt180) cc_final: 0.4859 (tmt170) REVERT: B 577 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7808 (mpt90) REVERT: B 596 THR cc_start: 0.6680 (t) cc_final: 0.6417 (p) REVERT: B 607 THR cc_start: 0.9379 (p) cc_final: 0.9155 (p) REVERT: B 629 ARG cc_start: 0.7738 (mtt180) cc_final: 0.6864 (ttm170) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2324 time to fit residues: 18.1545 Evaluate side-chains 47 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2192 Z= 0.153 Angle : 0.564 4.086 2958 Z= 0.292 Chirality : 0.043 0.191 352 Planarity : 0.004 0.043 372 Dihedral : 5.104 17.532 300 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.49), residues: 266 helix: -0.08 (0.60), residues: 80 sheet: -1.30 (0.91), residues: 25 loop : -1.16 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 570 HIS 0.003 0.001 HIS B 817 PHE 0.006 0.001 PHE A 810 TYR 0.014 0.002 TYR A 576 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6010 (tpt) cc_final: 0.5611 (tpt) REVERT: A 590 HIS cc_start: 0.9587 (p-80) cc_final: 0.9144 (p-80) REVERT: A 611 MET cc_start: 0.7686 (tpp) cc_final: 0.7374 (tpp) REVERT: A 836 ARG cc_start: 0.6162 (mmt180) cc_final: 0.4804 (tmt170) REVERT: B 577 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7764 (mpt90) REVERT: B 596 THR cc_start: 0.6578 (t) cc_final: 0.6352 (p) REVERT: B 607 THR cc_start: 0.9391 (p) cc_final: 0.9187 (p) REVERT: B 629 ARG cc_start: 0.7688 (mtt180) cc_final: 0.6790 (ttm170) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2032 time to fit residues: 15.6712 Evaluate side-chains 49 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2192 Z= 0.181 Angle : 0.579 5.942 2958 Z= 0.301 Chirality : 0.043 0.152 352 Planarity : 0.004 0.041 372 Dihedral : 5.162 18.992 300 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.50), residues: 266 helix: -0.26 (0.58), residues: 81 sheet: -1.71 (0.88), residues: 25 loop : -1.17 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.002 0.001 HIS B 817 PHE 0.005 0.001 PHE A 810 TYR 0.006 0.001 TYR B 819 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 HIS cc_start: 0.9554 (p-80) cc_final: 0.9126 (p-80) REVERT: A 836 ARG cc_start: 0.6166 (mmt180) cc_final: 0.4789 (tmt170) REVERT: B 577 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7770 (mpt90) REVERT: B 581 GLU cc_start: 0.8733 (tt0) cc_final: 0.8374 (tt0) REVERT: B 596 THR cc_start: 0.6648 (t) cc_final: 0.6441 (p) REVERT: B 607 THR cc_start: 0.9366 (p) cc_final: 0.9165 (p) REVERT: B 629 ARG cc_start: 0.7674 (mtt180) cc_final: 0.6810 (ttm170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2104 time to fit residues: 15.0901 Evaluate side-chains 48 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2192 Z= 0.158 Angle : 0.579 5.611 2958 Z= 0.296 Chirality : 0.042 0.141 352 Planarity : 0.004 0.039 372 Dihedral : 4.968 19.489 300 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.51), residues: 266 helix: -0.20 (0.59), residues: 81 sheet: -1.68 (0.91), residues: 25 loop : -1.06 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.004 0.001 HIS A 807 PHE 0.004 0.001 PHE B 795 TYR 0.006 0.001 TYR B 819 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 HIS cc_start: 0.9531 (p-80) cc_final: 0.9110 (p-80) REVERT: A 611 MET cc_start: 0.7703 (tpp) cc_final: 0.7381 (tpp) REVERT: A 836 ARG cc_start: 0.6067 (mmt180) cc_final: 0.4780 (tmt170) REVERT: B 577 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7791 (mpt90) REVERT: B 596 THR cc_start: 0.6842 (t) cc_final: 0.6623 (p) REVERT: B 629 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6814 (ttm170) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2171 time to fit residues: 16.1816 Evaluate side-chains 44 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2192 Z= 0.155 Angle : 0.586 5.173 2958 Z= 0.303 Chirality : 0.043 0.134 352 Planarity : 0.004 0.036 372 Dihedral : 4.853 20.235 300 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.51), residues: 266 helix: -0.15 (0.58), residues: 81 sheet: -1.60 (0.92), residues: 25 loop : -1.12 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 807 PHE 0.004 0.001 PHE A 810 TYR 0.008 0.001 TYR B 819 ARG 0.011 0.000 ARG A 825 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 HIS cc_start: 0.9505 (p-80) cc_final: 0.9101 (p-80) REVERT: A 836 ARG cc_start: 0.6293 (mmt180) cc_final: 0.4924 (tmt170) REVERT: B 577 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7791 (mpt90) REVERT: B 629 ARG cc_start: 0.7673 (mtt180) cc_final: 0.6811 (ttm170) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2081 time to fit residues: 15.3674 Evaluate side-chains 47 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2192 Z= 0.220 Angle : 0.658 5.141 2958 Z= 0.342 Chirality : 0.044 0.139 352 Planarity : 0.005 0.037 372 Dihedral : 5.181 20.155 300 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.51), residues: 266 helix: -0.27 (0.59), residues: 80 sheet: -2.54 (0.74), residues: 35 loop : -0.98 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 570 HIS 0.004 0.001 HIS B 817 PHE 0.006 0.001 PHE A 810 TYR 0.008 0.002 TYR B 819 ARG 0.006 0.000 ARG A 825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 ASP cc_start: 0.8130 (p0) cc_final: 0.7831 (p0) REVERT: A 590 HIS cc_start: 0.9521 (p-80) cc_final: 0.9153 (p-80) REVERT: A 611 MET cc_start: 0.7731 (tpp) cc_final: 0.7394 (tpp) REVERT: A 836 ARG cc_start: 0.6631 (mmt180) cc_final: 0.4940 (tmt170) REVERT: B 607 THR cc_start: 0.9293 (p) cc_final: 0.9070 (p) REVERT: B 629 ARG cc_start: 0.7703 (mtt180) cc_final: 0.6676 (ttm170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1935 time to fit residues: 14.7783 Evaluate side-chains 48 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 0.0050 chunk 21 optimal weight: 0.0060 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2192 Z= 0.163 Angle : 0.617 6.650 2958 Z= 0.316 Chirality : 0.043 0.136 352 Planarity : 0.004 0.035 372 Dihedral : 4.755 19.770 300 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.51), residues: 266 helix: -0.12 (0.59), residues: 82 sheet: -2.30 (0.73), residues: 35 loop : -1.08 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 570 HIS 0.003 0.001 HIS A 817 PHE 0.004 0.001 PHE B 810 TYR 0.007 0.001 TYR B 819 ARG 0.004 0.000 ARG A 825 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 HIS cc_start: 0.9473 (p-80) cc_final: 0.9101 (p-80) REVERT: A 611 MET cc_start: 0.7655 (tpp) cc_final: 0.7310 (tpp) REVERT: A 836 ARG cc_start: 0.6060 (mmt180) cc_final: 0.4789 (tmt170) REVERT: B 577 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7819 (mpt90) REVERT: B 581 GLU cc_start: 0.8594 (tt0) cc_final: 0.8182 (tt0) REVERT: B 629 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6766 (ttm170) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1944 time to fit residues: 14.5189 Evaluate side-chains 47 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6970 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.159221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140267 restraints weight = 5712.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143339 restraints weight = 3647.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.145326 restraints weight = 2598.602| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2192 Z= 0.168 Angle : 0.596 4.839 2958 Z= 0.306 Chirality : 0.044 0.131 352 Planarity : 0.004 0.037 372 Dihedral : 4.750 20.966 300 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.52), residues: 266 helix: -0.12 (0.59), residues: 82 sheet: -2.48 (0.72), residues: 35 loop : -1.03 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 570 HIS 0.003 0.001 HIS A 807 PHE 0.004 0.001 PHE A 785 TYR 0.008 0.001 TYR B 819 ARG 0.004 0.000 ARG A 825 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.75 seconds wall clock time: 21 minutes 16.91 seconds (1276.91 seconds total)