Starting phenix.real_space_refine on Fri Aug 22 15:51:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gim_51374/08_2025/9gim_51374.map" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 3410 2.51 5 N 918 2.21 5 O 971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5321 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 40, 'TRANS': 598} Chain breaks: 2 Time building chain proxies: 1.35, per 1000 atoms: 0.25 Number of scatterers: 5321 At special positions: 0 Unit cell: (75.024, 79.192, 114.203, 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 971 8.00 N 918 7.00 C 3410 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: 0.46 Conformation dependent library (CDL) restraints added in 210.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 36.0% alpha, 16.6% 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 232 through 252 removed outlier: 3.677A pdb=" N ARG A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.543A pdb=" N LYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.553A pdb=" N SER A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.691A pdb=" N VAL A 623 " --> pdb=" O ARG A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 656 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.894A pdb=" N CYS A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 704 removed outlier: 3.573A pdb=" N TYR A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 3.735A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 733 through 746 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.970A pdb=" N GLU A 750 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 800 through 813 Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.576A pdb=" N LEU A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 820 " --> pdb=" O ILE A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 857 through 870 Processing helix chain 'A' and resid 871 through 884 Processing helix chain 'A' and resid 892 through 895 removed outlier: 3.975A pdb=" N GLU A 895 " --> pdb=" O GLY A 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 892 through 895' Processing helix chain 'A' and resid 933 through 947 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 6.893A pdb=" N ARG A 147 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 29 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 145 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 63 removed outlier: 7.094A pdb=" N GLU A 57 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 51 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 45 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 95 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 104 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.797A pdb=" N ILE A 553 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 602 Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA7, first strand: chain 'A' and resid 757 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AA9, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.744A pdb=" N GLY A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 573 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: 0.87 Time building geometry restraints manager: 0.63 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: 1748 1.34 - 1.46: 1173 1.46 - 1.58: 2505 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5465 Sorted by residual: bond pdb=" CB PRO A 72 " pdb=" CG PRO A 72 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.81e-01 bond pdb=" C MET A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.25e-02 6.40e+03 4.49e-01 bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.545 1.539 0.006 9.10e-03 1.21e+04 4.28e-01 bond pdb=" CA VAL A 229 " pdb=" CB VAL A 229 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.04e-01 bond pdb=" CB TRP A 74 " pdb=" CG TRP A 74 " ideal model delta sigma weight residual 1.498 1.479 0.019 3.10e-02 1.04e+03 3.94e-01 ... (remaining 5460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 7109 1.03 - 2.05: 213 2.05 - 3.08: 59 3.08 - 4.11: 9 4.11 - 5.13: 5 Bond angle restraints: 7395 Sorted by residual: angle pdb=" C ASP A 228 " pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 121.97 125.75 -3.78 1.80e+00 3.09e-01 4.40e+00 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" CB THR A 121 " ideal model delta sigma weight residual 113.65 110.66 2.99 1.47e+00 4.63e-01 4.13e+00 angle pdb=" C ARG A 560 " pdb=" N LEU A 561 " pdb=" CA LEU A 561 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.96e+00 angle pdb=" N MET A 153 " pdb=" CA MET A 153 " pdb=" C MET A 153 " ideal model delta sigma weight residual 109.81 114.08 -4.27 2.21e+00 2.05e-01 3.73e+00 angle pdb=" C VAL A 26 " pdb=" N VAL A 27 " pdb=" CA VAL A 27 " ideal model delta sigma weight residual 122.97 121.09 1.88 9.80e-01 1.04e+00 3.68e+00 ... (remaining 7390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.37: 2894 10.37 - 20.73: 269 20.73 - 31.10: 82 31.10 - 41.46: 38 41.46 - 51.83: 7 Dihedral angle restraints: 3290 sinusoidal: 1414 harmonic: 1876 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA HIS A 549 " pdb=" C HIS A 549 " pdb=" N ASN A 550 " pdb=" CA ASN A 550 " ideal model delta harmonic sigma weight residual 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.73e+00 dihedral pdb=" CA LEU A 835 " pdb=" CB LEU A 835 " pdb=" CG LEU A 835 " pdb=" CD1 LEU A 835 " ideal model delta sinusoidal sigma weight residual 180.00 128.63 51.37 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 3287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 418 0.026 - 0.051: 245 0.051 - 0.077: 50 0.077 - 0.102: 34 0.102 - 0.128: 17 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ILE A 566 " pdb=" N ILE A 566 " pdb=" C ILE A 566 " pdb=" CB ILE A 566 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 761 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 528 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 529 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 594 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 595 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 857 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 858 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 858 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 858 " 0.019 5.00e-02 4.00e+02 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1020 2.77 - 3.31: 5123 3.31 - 3.84: 8349 3.84 - 4.37: 9504 4.37 - 4.90: 16324 Nonbonded interactions: 40320 Sorted by model distance: nonbonded pdb=" NH1 ARG A 253 " pdb=" OD1 ASP A 258 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A 612 " pdb=" OG SER A 688 " model vdw 2.253 3.040 nonbonded pdb=" O ARG A 248 " pdb=" OG SER A 251 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 849 " pdb=" NE1 TRP A 864 " model vdw 2.301 3.120 nonbonded pdb=" OE2 GLU A 535 " pdb=" NE2 HIS A 549 " model vdw 2.338 3.120 ... (remaining 40315 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: 3.990 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.002 0.038 5465 Z= 0.108 Angle : 0.479 5.133 7395 Z= 0.250 Chirality : 0.038 0.128 764 Planarity : 0.004 0.047 968 Dihedral : 10.035 51.827 2078 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 1.71 % Allowed : 4.79 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.34), residues: 633 helix: 0.55 (0.37), residues: 190 sheet: -0.26 (0.44), residues: 121 loop : -1.06 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 537 TYR 0.006 0.001 TYR A 44 PHE 0.015 0.001 PHE A 692 TRP 0.007 0.001 TRP A 862 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5465) covalent geometry : angle 0.47934 ( 7395) hydrogen bonds : bond 0.14919 ( 208) hydrogen bonds : angle 5.93364 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7797 (t0) cc_final: 0.7426 (t0) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0995 time to fit residues: 9.5243 Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 71 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 254 HIS A 603 HIS A 767 GLN A 861 GLN A 891 ASN A 909 GLN A 924 ASN A 949 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088347 restraints weight = 13174.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087676 restraints weight = 15124.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088609 restraints weight = 11874.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088649 restraints weight = 10710.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088766 restraints weight = 9107.227| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5465 Z= 0.154 Angle : 0.570 9.760 7395 Z= 0.292 Chirality : 0.042 0.155 764 Planarity : 0.004 0.046 968 Dihedral : 3.983 26.207 709 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 0.17 % Allowed : 2.05 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.34), residues: 633 helix: 0.64 (0.37), residues: 187 sheet: -0.39 (0.45), residues: 125 loop : -1.16 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 695 TYR 0.019 0.001 TYR A 152 PHE 0.018 0.002 PHE A 692 TRP 0.015 0.001 TRP A 74 HIS 0.004 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5465) covalent geometry : angle 0.56963 ( 7395) hydrogen bonds : bond 0.04248 ( 208) hydrogen bonds : angle 5.20556 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7867 (t0) cc_final: 0.7505 (t0) REVERT: A 582 ASP cc_start: 0.6745 (t0) cc_final: 0.6506 (t70) REVERT: A 847 SER cc_start: 0.8744 (m) cc_final: 0.8537 (p) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.0657 time to fit residues: 5.7355 Evaluate side-chains 52 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS A 826 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.110389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086549 restraints weight = 12894.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086130 restraints weight = 12026.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086539 restraints weight = 10147.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086811 restraints weight = 9113.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086887 restraints weight = 8423.495| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5465 Z= 0.168 Angle : 0.581 9.140 7395 Z= 0.294 Chirality : 0.042 0.124 764 Planarity : 0.004 0.046 968 Dihedral : 4.152 27.549 709 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.95 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.34), residues: 633 helix: 0.36 (0.36), residues: 193 sheet: -0.64 (0.44), residues: 127 loop : -1.24 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 695 TYR 0.019 0.001 TYR A 849 PHE 0.022 0.002 PHE A 692 TRP 0.015 0.001 TRP A 74 HIS 0.005 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5465) covalent geometry : angle 0.58142 ( 7395) hydrogen bonds : bond 0.03843 ( 208) hydrogen bonds : angle 5.26481 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5864 (mpp) cc_final: 0.5444 (mmt) REVERT: A 138 HIS cc_start: 0.7914 (p-80) cc_final: 0.7705 (p90) REVERT: A 563 ASN cc_start: 0.7854 (t0) cc_final: 0.7535 (t0) REVERT: A 582 ASP cc_start: 0.6783 (t0) cc_final: 0.6537 (t70) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0772 time to fit residues: 6.3205 Evaluate side-chains 50 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087734 restraints weight = 12966.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086589 restraints weight = 11328.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087021 restraints weight = 10076.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087113 restraints weight = 8917.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087223 restraints weight = 8537.051| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5465 Z= 0.179 Angle : 0.593 10.017 7395 Z= 0.297 Chirality : 0.041 0.128 764 Planarity : 0.004 0.047 968 Dihedral : 4.287 29.678 709 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.95 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.33), residues: 633 helix: 0.22 (0.36), residues: 193 sheet: -0.70 (0.44), residues: 125 loop : -1.32 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 575 TYR 0.014 0.001 TYR A 849 PHE 0.029 0.002 PHE A 648 TRP 0.017 0.002 TRP A 74 HIS 0.005 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5465) covalent geometry : angle 0.59302 ( 7395) hydrogen bonds : bond 0.03698 ( 208) hydrogen bonds : angle 5.26344 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5385 (mpp) cc_final: 0.4739 (mpp) REVERT: A 153 MET cc_start: 0.6325 (mtt) cc_final: 0.5113 (mtt) REVERT: A 563 ASN cc_start: 0.7792 (t0) cc_final: 0.7458 (t0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0822 time to fit residues: 6.6219 Evaluate side-chains 44 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088183 restraints weight = 13377.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087090 restraints weight = 11262.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087275 restraints weight = 10089.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087425 restraints weight = 8999.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087543 restraints weight = 8364.819| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5465 Z= 0.140 Angle : 0.558 9.261 7395 Z= 0.281 Chirality : 0.041 0.141 764 Planarity : 0.004 0.048 968 Dihedral : 4.242 27.697 709 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.33), residues: 633 helix: 0.39 (0.37), residues: 193 sheet: -0.75 (0.45), residues: 125 loop : -1.32 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 695 TYR 0.012 0.001 TYR A 849 PHE 0.019 0.001 PHE A 692 TRP 0.018 0.001 TRP A 74 HIS 0.004 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5465) covalent geometry : angle 0.55836 ( 7395) hydrogen bonds : bond 0.03440 ( 208) hydrogen bonds : angle 5.14884 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5280 (mpp) cc_final: 0.4686 (mpp) REVERT: A 153 MET cc_start: 0.6366 (mtt) cc_final: 0.5782 (mtt) REVERT: A 563 ASN cc_start: 0.7841 (t0) cc_final: 0.7526 (t0) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0701 time to fit residues: 5.6025 Evaluate side-chains 45 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084724 restraints weight = 13373.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083780 restraints weight = 14055.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.084203 restraints weight = 11730.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084441 restraints weight = 10818.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084576 restraints weight = 9741.198| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5465 Z= 0.185 Angle : 0.603 9.151 7395 Z= 0.303 Chirality : 0.042 0.160 764 Planarity : 0.004 0.046 968 Dihedral : 4.352 26.788 709 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.58 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.33), residues: 633 helix: -0.04 (0.35), residues: 193 sheet: -0.83 (0.44), residues: 127 loop : -1.40 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 938 TYR 0.011 0.001 TYR A 849 PHE 0.027 0.002 PHE A 648 TRP 0.023 0.002 TRP A 74 HIS 0.005 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5465) covalent geometry : angle 0.60336 ( 7395) hydrogen bonds : bond 0.03711 ( 208) hydrogen bonds : angle 5.31522 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5214 (mpp) cc_final: 0.4707 (mpp) REVERT: A 153 MET cc_start: 0.6611 (mtt) cc_final: 0.5997 (mtt) REVERT: A 563 ASN cc_start: 0.7879 (t0) cc_final: 0.7549 (t0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0665 time to fit residues: 5.0376 Evaluate side-chains 43 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088111 restraints weight = 13168.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086506 restraints weight = 11879.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086710 restraints weight = 10750.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086957 restraints weight = 9508.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087058 restraints weight = 8841.441| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5465 Z= 0.133 Angle : 0.557 8.818 7395 Z= 0.282 Chirality : 0.041 0.144 764 Planarity : 0.004 0.048 968 Dihedral : 4.276 26.178 709 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.33), residues: 633 helix: 0.26 (0.37), residues: 193 sheet: -0.76 (0.44), residues: 127 loop : -1.38 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 844 TYR 0.010 0.001 TYR A 79 PHE 0.018 0.001 PHE A 692 TRP 0.036 0.002 TRP A 864 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5465) covalent geometry : angle 0.55735 ( 7395) hydrogen bonds : bond 0.03307 ( 208) hydrogen bonds : angle 5.14193 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5153 (mpp) cc_final: 0.4698 (mpp) REVERT: A 153 MET cc_start: 0.6400 (mtt) cc_final: 0.5918 (mtt) REVERT: A 563 ASN cc_start: 0.7807 (t0) cc_final: 0.7477 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0963 time to fit residues: 7.1341 Evaluate side-chains 43 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087370 restraints weight = 13053.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086792 restraints weight = 12241.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087175 restraints weight = 9907.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087264 restraints weight = 8848.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087475 restraints weight = 8493.283| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5465 Z= 0.122 Angle : 0.551 8.826 7395 Z= 0.274 Chirality : 0.040 0.141 764 Planarity : 0.004 0.051 968 Dihedral : 4.265 25.596 709 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.33), residues: 633 helix: 0.41 (0.37), residues: 193 sheet: -0.82 (0.44), residues: 127 loop : -1.38 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 614 TYR 0.009 0.001 TYR A 849 PHE 0.016 0.001 PHE A 692 TRP 0.029 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5465) covalent geometry : angle 0.55106 ( 7395) hydrogen bonds : bond 0.03162 ( 208) hydrogen bonds : angle 5.03206 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5081 (mpp) cc_final: 0.4670 (mpp) REVERT: A 153 MET cc_start: 0.6404 (mtt) cc_final: 0.5900 (mtt) REVERT: A 563 ASN cc_start: 0.7758 (t0) cc_final: 0.7434 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0827 time to fit residues: 6.2743 Evaluate side-chains 44 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.0010 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088299 restraints weight = 13176.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086911 restraints weight = 11376.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087099 restraints weight = 9576.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087199 restraints weight = 9887.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087278 restraints weight = 8632.873| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5465 Z= 0.130 Angle : 0.551 8.773 7395 Z= 0.277 Chirality : 0.040 0.134 764 Planarity : 0.004 0.050 968 Dihedral : 4.242 25.406 709 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.79 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.33), residues: 633 helix: 0.55 (0.37), residues: 187 sheet: -0.81 (0.44), residues: 127 loop : -1.38 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 614 TYR 0.009 0.001 TYR A 849 PHE 0.018 0.001 PHE A 692 TRP 0.026 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5465) covalent geometry : angle 0.55058 ( 7395) hydrogen bonds : bond 0.03141 ( 208) hydrogen bonds : angle 5.07496 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5159 (mpp) cc_final: 0.4712 (mpp) REVERT: A 153 MET cc_start: 0.6546 (mtt) cc_final: 0.5959 (mtt) REVERT: A 563 ASN cc_start: 0.7840 (t0) cc_final: 0.7516 (t0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0769 time to fit residues: 5.8155 Evaluate side-chains 42 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.110021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087922 restraints weight = 13316.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086217 restraints weight = 14475.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087188 restraints weight = 13649.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087475 restraints weight = 10604.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087855 restraints weight = 9144.129| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5465 Z= 0.155 Angle : 0.581 8.787 7395 Z= 0.290 Chirality : 0.041 0.160 764 Planarity : 0.004 0.051 968 Dihedral : 4.339 25.412 709 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.33), residues: 633 helix: 0.20 (0.36), residues: 193 sheet: -1.04 (0.43), residues: 130 loop : -1.33 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 844 TYR 0.010 0.001 TYR A 849 PHE 0.021 0.002 PHE A 692 TRP 0.025 0.002 TRP A 74 HIS 0.005 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5465) covalent geometry : angle 0.58126 ( 7395) hydrogen bonds : bond 0.03280 ( 208) hydrogen bonds : angle 5.16383 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5185 (mpp) cc_final: 0.4777 (mpp) REVERT: A 153 MET cc_start: 0.6165 (mtt) cc_final: 0.5763 (mtt) REVERT: A 563 ASN cc_start: 0.7682 (t0) cc_final: 0.7368 (t0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0818 time to fit residues: 6.0202 Evaluate side-chains 42 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088165 restraints weight = 13312.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086843 restraints weight = 12246.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087342 restraints weight = 11302.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087523 restraints weight = 10288.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087742 restraints weight = 9110.003| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5465 Z= 0.120 Angle : 0.554 8.644 7395 Z= 0.276 Chirality : 0.041 0.165 764 Planarity : 0.004 0.051 968 Dihedral : 4.228 25.167 709 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.33), residues: 633 helix: 0.61 (0.37), residues: 186 sheet: -1.04 (0.43), residues: 130 loop : -1.31 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.008 0.001 TYR A 849 PHE 0.027 0.001 PHE A 648 TRP 0.026 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5465) covalent geometry : angle 0.55388 ( 7395) hydrogen bonds : bond 0.03093 ( 208) hydrogen bonds : angle 5.08392 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 974.31 seconds wall clock time: 17 minutes 29.66 seconds (1049.66 seconds total)