Starting phenix.real_space_refine on Wed Jun 4 10:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.map" model { file = "/net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9noy_49621/06_2025/9noy_49621.cif" } resolution = 3.7 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= 0.010 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 22 5.16 5 C 1355 2.51 5 N 315 2.21 5 O 339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2031 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Time building chain proxies: 2.86, per 1000 atoms: 1.41 Number of scatterers: 2031 At special positions: 0 Unit cell: (56.787, 51.026, 76.539, 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 22 16.00 O 339 8.00 N 315 7.00 C 1355 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: 0.58 Conformation dependent library (CDL) restraints added in 264.3 milliseconds 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 490 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 89.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 601 through 617 removed outlier: 3.748A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.661A pdb=" N TYR A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.270A pdb=" N GLN A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.566A pdb=" N TYR A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 670 " --> pdb=" O PRO A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.799A pdb=" N MET A 682 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.751A pdb=" N PHE A 730 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.177A pdb=" N SER A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.370A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 822 Processing helix chain 'A' and resid 823 through 836 160 hydrogen bonds defined for protein. 477 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: 0.51 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 590 1.34 - 1.46: 536 1.46 - 1.58: 925 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 2086 Sorted by residual: bond pdb=" CB ILE A 815 " pdb=" CG2 ILE A 815 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 5.99e-01 bond pdb=" CA VAL A 618 " pdb=" CB VAL A 618 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.49e-01 bond pdb=" CB VAL A 569 " pdb=" CG1 VAL A 569 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.26e-01 bond pdb=" CG GLU A 560 " pdb=" CD GLU A 560 " ideal model delta sigma weight residual 1.516 1.530 -0.014 2.50e-02 1.60e+03 2.95e-01 bond pdb=" CG LEU A 816 " pdb=" CD2 LEU A 816 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.64e-01 ... (remaining 2081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2746 1.44 - 2.88: 74 2.88 - 4.32: 14 4.32 - 5.76: 6 5.76 - 7.20: 1 Bond angle restraints: 2841 Sorted by residual: angle pdb=" C VAL A 786 " pdb=" N LEU A 787 " pdb=" CA LEU A 787 " ideal model delta sigma weight residual 121.54 126.04 -4.50 1.91e+00 2.74e-01 5.56e+00 angle pdb=" CA LEU A 794 " pdb=" CB LEU A 794 " pdb=" CG LEU A 794 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" C GLU A 563 " pdb=" CA GLU A 563 " pdb=" CB GLU A 563 " ideal model delta sigma weight residual 109.86 113.32 -3.46 1.80e+00 3.09e-01 3.70e+00 angle pdb=" C PHE A 591 " pdb=" N GLN A 592 " pdb=" CA GLN A 592 " ideal model delta sigma weight residual 122.08 124.47 -2.39 1.47e+00 4.63e-01 2.65e+00 angle pdb=" C TYR A 807 " pdb=" N PHE A 808 " pdb=" CA PHE A 808 " ideal model delta sigma weight residual 122.36 119.78 2.58 1.72e+00 3.38e-01 2.25e+00 ... (remaining 2836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 998 15.85 - 31.71: 161 31.71 - 47.56: 49 47.56 - 63.42: 12 63.42 - 79.27: 2 Dihedral angle restraints: 1222 sinusoidal: 461 harmonic: 761 Sorted by residual: dihedral pdb=" CA GLU A 563 " pdb=" C GLU A 563 " pdb=" N ALA A 564 " pdb=" CA ALA A 564 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" N MET A 682 " pdb=" CA MET A 682 " pdb=" CB MET A 682 " pdb=" CG MET A 682 " ideal model delta sinusoidal sigma weight residual -180.00 -121.41 -58.59 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 597 " pdb=" CB ARG A 597 " pdb=" CG ARG A 597 " pdb=" CD ARG A 597 " ideal model delta sinusoidal sigma weight residual -180.00 -122.99 -57.01 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 187 0.027 - 0.053: 92 0.053 - 0.080: 38 0.080 - 0.106: 17 0.106 - 0.133: 3 Chirality restraints: 337 Sorted by residual: chirality pdb=" CB THR A 609 " pdb=" CA THR A 609 " pdb=" OG1 THR A 609 " pdb=" CG2 THR A 609 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" C PRO A 565 " pdb=" CB PRO A 565 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA MET A 661 " pdb=" N MET A 661 " pdb=" C MET A 661 " pdb=" CB MET A 661 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.08e-01 ... (remaining 334 not shown) Planarity restraints: 341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 561 " 0.014 2.00e-02 2.50e+03 1.64e-02 6.71e+00 pdb=" CG TRP A 561 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 561 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 561 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 561 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 561 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 561 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 561 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 561 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 561 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 564 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 565 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 809 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 810 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.019 5.00e-02 4.00e+02 ... (remaining 338 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 1473 3.08 - 3.54: 2421 3.54 - 3.99: 2849 3.99 - 4.44: 3692 4.44 - 4.90: 5315 Nonbonded interactions: 15750 Sorted by model distance: nonbonded pdb=" C SER A 579 " pdb=" OG SER A 579 " model vdw 2.625 2.616 nonbonded pdb=" N PHE A 591 " pdb=" O PHE A 591 " model vdw 2.642 2.496 nonbonded pdb=" O VAL A 656 " pdb=" O LYS A 660 " model vdw 2.643 3.040 nonbonded pdb=" N TYR A 783 " pdb=" O TYR A 783 " model vdw 2.649 2.496 nonbonded pdb=" C SER A 775 " pdb=" OG SER A 775 " model vdw 2.655 2.616 ... (remaining 15745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.960 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: 11.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.003 0.026 2086 Z= 0.135 Angle : 0.605 7.202 2841 Z= 0.301 Chirality : 0.040 0.133 337 Planarity : 0.005 0.047 341 Dihedral : 17.430 79.271 732 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.33 % Allowed : 33.33 % Favored : 65.33 % 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: 1.89 (0.53), residues: 253 helix: 1.66 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -0.27 (0.82), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 561 HIS 0.002 0.001 HIS A 562 PHE 0.022 0.001 PHE A 684 TYR 0.007 0.001 TYR A 834 ARG 0.002 0.000 ARG A 597 Details of bonding type rmsd hydrogen bonds : bond 0.14387 ( 160) hydrogen bonds : angle 5.63297 ( 477) covalent geometry : bond 0.00303 ( 2086) covalent geometry : angle 0.60537 ( 2841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 690 MET cc_start: 0.7373 (ppp) cc_final: 0.6997 (ppp) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.1207 time to fit residues: 9.6689 Evaluate side-chains 63 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 688 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.134488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117758 restraints weight = 3998.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120975 restraints weight = 2193.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123303 restraints weight = 1441.968| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2086 Z= 0.141 Angle : 0.590 9.755 2841 Z= 0.291 Chirality : 0.040 0.121 337 Planarity : 0.005 0.047 341 Dihedral : 5.895 56.495 288 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.78 % Allowed : 31.11 % Favored : 63.11 % 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: 2.44 (0.53), residues: 253 helix: 2.06 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -0.08 (0.79), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.015 0.001 PHE A 684 TYR 0.011 0.001 TYR A 669 ARG 0.002 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 160) hydrogen bonds : angle 4.17127 ( 477) covalent geometry : bond 0.00318 ( 2086) covalent geometry : angle 0.58997 ( 2841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.212 Fit side-chains REVERT: A 563 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 657 CYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (t) REVERT: A 660 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (ttpt) REVERT: A 682 MET cc_start: 0.7614 (tmm) cc_final: 0.6784 (tmm) REVERT: A 690 MET cc_start: 0.7684 (ppp) cc_final: 0.7154 (ppp) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 0.1064 time to fit residues: 9.0175 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.133281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116572 restraints weight = 3940.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119873 restraints weight = 2151.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122062 restraints weight = 1408.045| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2086 Z= 0.150 Angle : 0.599 8.733 2841 Z= 0.294 Chirality : 0.039 0.124 337 Planarity : 0.005 0.043 341 Dihedral : 5.733 57.109 286 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 7.11 % Allowed : 31.56 % Favored : 61.33 % 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: 2.45 (0.53), residues: 253 helix: 2.11 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -0.35 (0.78), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.013 0.001 PHE A 745 TYR 0.010 0.001 TYR A 621 ARG 0.002 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 160) hydrogen bonds : angle 4.00817 ( 477) covalent geometry : bond 0.00344 ( 2086) covalent geometry : angle 0.59946 ( 2841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.221 Fit side-chains REVERT: A 563 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 621 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6743 (t80) REVERT: A 657 CYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8142 (t) REVERT: A 682 MET cc_start: 0.7546 (tmm) cc_final: 0.6635 (tmm) REVERT: A 690 MET cc_start: 0.7771 (ppp) cc_final: 0.7293 (ppp) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.1128 time to fit residues: 9.7521 Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 795 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119421 restraints weight = 3854.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122819 restraints weight = 2092.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125085 restraints weight = 1366.295| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2086 Z= 0.112 Angle : 0.604 7.979 2841 Z= 0.283 Chirality : 0.037 0.106 337 Planarity : 0.005 0.040 341 Dihedral : 5.531 58.874 286 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.44 % Allowed : 36.00 % Favored : 59.56 % 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: 2.76 (0.54), residues: 253 helix: 2.22 (0.37), residues: 206 sheet: None (None), residues: 0 loop : 0.09 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.016 0.001 PHE A 684 TYR 0.011 0.001 TYR A 621 ARG 0.001 0.000 ARG A 674 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 160) hydrogen bonds : angle 3.90630 ( 477) covalent geometry : bond 0.00249 ( 2086) covalent geometry : angle 0.60395 ( 2841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.214 Fit side-chains REVERT: A 621 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6623 (t80) REVERT: A 657 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 682 MET cc_start: 0.7531 (tmm) cc_final: 0.6545 (tmm) REVERT: A 690 MET cc_start: 0.7809 (ppp) cc_final: 0.7333 (ppp) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.1086 time to fit residues: 9.3492 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 4 optimal weight: 0.0980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119152 restraints weight = 3979.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122500 restraints weight = 2143.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124789 restraints weight = 1408.814| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2086 Z= 0.116 Angle : 0.633 8.045 2841 Z= 0.298 Chirality : 0.039 0.154 337 Planarity : 0.005 0.052 341 Dihedral : 5.511 58.588 286 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.67 % Allowed : 34.22 % Favored : 59.11 % 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: 2.78 (0.54), residues: 253 helix: 2.25 (0.37), residues: 206 sheet: None (None), residues: 0 loop : 0.05 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.019 0.001 PHE A 761 TYR 0.009 0.001 TYR A 621 ARG 0.001 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 160) hydrogen bonds : angle 3.82080 ( 477) covalent geometry : bond 0.00260 ( 2086) covalent geometry : angle 0.63291 ( 2841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.215 Fit side-chains REVERT: A 621 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 657 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8038 (t) REVERT: A 682 MET cc_start: 0.7545 (tmm) cc_final: 0.6456 (tmm) REVERT: A 690 MET cc_start: 0.7881 (ppp) cc_final: 0.7372 (ppp) REVERT: A 803 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8617 (tt) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 0.1418 time to fit residues: 11.3523 Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.133939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117579 restraints weight = 3980.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120838 restraints weight = 2158.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123157 restraints weight = 1421.867| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2086 Z= 0.147 Angle : 0.641 8.442 2841 Z= 0.304 Chirality : 0.039 0.123 337 Planarity : 0.006 0.053 341 Dihedral : 5.800 59.520 286 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.67 % Allowed : 34.22 % Favored : 59.11 % 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: 2.53 (0.54), residues: 253 helix: 2.03 (0.37), residues: 208 sheet: None (None), residues: 0 loop : 0.10 (0.91), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.013 0.001 PHE A 745 TYR 0.016 0.001 TYR A 621 ARG 0.006 0.001 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 160) hydrogen bonds : angle 3.85696 ( 477) covalent geometry : bond 0.00340 ( 2086) covalent geometry : angle 0.64122 ( 2841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.230 Fit side-chains REVERT: A 621 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 657 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8048 (t) REVERT: A 685 ILE cc_start: 0.9297 (tp) cc_final: 0.8896 (tp) REVERT: A 690 MET cc_start: 0.7927 (ppp) cc_final: 0.7412 (ppp) REVERT: A 803 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (tt) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.1258 time to fit residues: 10.7094 Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116494 restraints weight = 4055.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119759 restraints weight = 2204.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122078 restraints weight = 1431.368| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2086 Z= 0.165 Angle : 0.668 8.250 2841 Z= 0.321 Chirality : 0.040 0.139 337 Planarity : 0.005 0.054 341 Dihedral : 5.996 59.527 286 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 7.11 % Allowed : 33.33 % Favored : 59.56 % 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: 2.46 (0.54), residues: 253 helix: 2.00 (0.38), residues: 208 sheet: None (None), residues: 0 loop : 0.00 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 561 HIS 0.001 0.001 HIS A 562 PHE 0.017 0.001 PHE A 684 TYR 0.017 0.002 TYR A 621 ARG 0.006 0.001 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 160) hydrogen bonds : angle 3.86357 ( 477) covalent geometry : bond 0.00386 ( 2086) covalent geometry : angle 0.66759 ( 2841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.232 Fit side-chains REVERT: A 621 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6366 (t80) REVERT: A 657 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8076 (t) REVERT: A 685 ILE cc_start: 0.9308 (tp) cc_final: 0.8976 (tp) REVERT: A 690 MET cc_start: 0.8011 (ppp) cc_final: 0.7583 (ppp) REVERT: A 803 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 836 MET cc_start: 0.1890 (mmt) cc_final: 0.1244 (mmt) outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 0.1262 time to fit residues: 10.4586 Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.135100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118285 restraints weight = 4076.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121571 restraints weight = 2220.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123777 restraints weight = 1460.986| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2086 Z= 0.121 Angle : 0.644 8.277 2841 Z= 0.302 Chirality : 0.038 0.126 337 Planarity : 0.005 0.054 341 Dihedral : 5.792 57.734 286 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.78 % Allowed : 36.44 % Favored : 57.78 % 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: 2.60 (0.54), residues: 253 helix: 2.11 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.03 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.010 0.001 PHE A 761 TYR 0.014 0.001 TYR A 621 ARG 0.006 0.001 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 160) hydrogen bonds : angle 3.82282 ( 477) covalent geometry : bond 0.00273 ( 2086) covalent geometry : angle 0.64421 ( 2841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.212 Fit side-chains REVERT: A 621 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6312 (t80) REVERT: A 657 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7986 (t) REVERT: A 690 MET cc_start: 0.8042 (ppp) cc_final: 0.7522 (ppp) REVERT: A 803 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8567 (tt) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.1142 time to fit residues: 9.9809 Evaluate side-chains 73 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.135232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118366 restraints weight = 4158.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121693 restraints weight = 2214.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123899 restraints weight = 1435.755| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2086 Z= 0.123 Angle : 0.661 8.143 2841 Z= 0.313 Chirality : 0.039 0.128 337 Planarity : 0.005 0.056 341 Dihedral : 5.754 56.466 286 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.22 % Allowed : 36.89 % Favored : 56.89 % 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: 2.63 (0.54), residues: 253 helix: 2.13 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.00 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.009 0.001 PHE A 761 TYR 0.014 0.001 TYR A 621 ARG 0.005 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 160) hydrogen bonds : angle 3.79554 ( 477) covalent geometry : bond 0.00282 ( 2086) covalent geometry : angle 0.66077 ( 2841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.233 Fit side-chains REVERT: A 606 LEU cc_start: 0.9131 (tp) cc_final: 0.8835 (tp) REVERT: A 621 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 657 CYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7994 (t) REVERT: A 690 MET cc_start: 0.8096 (ppp) cc_final: 0.7557 (ppp) REVERT: A 803 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8570 (tt) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.1482 time to fit residues: 12.2203 Evaluate side-chains 73 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116758 restraints weight = 4020.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119883 restraints weight = 2187.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122059 restraints weight = 1456.112| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2086 Z= 0.151 Angle : 0.683 8.687 2841 Z= 0.324 Chirality : 0.040 0.125 337 Planarity : 0.006 0.057 341 Dihedral : 5.812 54.836 286 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.67 % Allowed : 36.00 % Favored : 57.33 % 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: 2.63 (0.55), residues: 253 helix: 2.08 (0.38), residues: 208 sheet: None (None), residues: 0 loop : 0.22 (0.92), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 561 HIS 0.000 0.000 HIS A 562 PHE 0.009 0.001 PHE A 591 TYR 0.016 0.002 TYR A 621 ARG 0.005 0.001 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 160) hydrogen bonds : angle 3.83502 ( 477) covalent geometry : bond 0.00356 ( 2086) covalent geometry : angle 0.68296 ( 2841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.225 Fit side-chains REVERT: A 561 TRP cc_start: 0.7182 (m100) cc_final: 0.6937 (m100) REVERT: A 606 LEU cc_start: 0.9161 (tp) cc_final: 0.8868 (tp) REVERT: A 621 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6427 (t80) REVERT: A 690 MET cc_start: 0.8178 (ppp) cc_final: 0.7655 (ppp) REVERT: A 780 MET cc_start: 0.8275 (mmm) cc_final: 0.7988 (mmm) REVERT: A 803 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8606 (tt) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.1208 time to fit residues: 10.1028 Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 832 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.134134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117355 restraints weight = 4012.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120608 restraints weight = 2149.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122798 restraints weight = 1408.724| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2086 Z= 0.151 Angle : 0.695 8.578 2841 Z= 0.328 Chirality : 0.039 0.133 337 Planarity : 0.006 0.057 341 Dihedral : 5.849 54.522 286 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.89 % Allowed : 36.89 % Favored : 58.22 % 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: 2.58 (0.55), residues: 253 helix: 2.05 (0.38), residues: 208 sheet: None (None), residues: 0 loop : 0.19 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 561 HIS 0.001 0.000 HIS A 562 PHE 0.008 0.001 PHE A 591 TYR 0.039 0.002 TYR A 807 ARG 0.005 0.001 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 160) hydrogen bonds : angle 3.86567 ( 477) covalent geometry : bond 0.00361 ( 2086) covalent geometry : angle 0.69468 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.23 seconds wall clock time: 23 minutes 4.04 seconds (1384.04 seconds total)