Starting phenix.real_space_refine on Fri Dec 27 04:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.map" model { file = "/net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pij_17683/12_2024/8pij_17683.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.02, per 1000 atoms: 1.38 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 391.1 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 24.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.404A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.906A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.582A pdb=" N VAL B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 222 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: 0.50 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA MET B 116 " pdb=" C MET B 116 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" CA VAL B 110 " pdb=" C VAL B 110 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" CA SER B 115 " pdb=" C SER B 115 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.34e-02 5.57e+03 5.89e+00 bond pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 1.521 1.497 0.025 1.23e-02 6.61e+03 3.99e+00 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2968 1.85 - 3.70: 40 3.70 - 5.55: 8 5.55 - 7.40: 2 7.40 - 9.25: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 1217 24.62 - 49.23: 108 49.23 - 73.84: 26 73.84 - 98.46: 0 98.46 - 123.07: 2 Dihedral angle restraints: 1353 sinusoidal: 524 harmonic: 829 Sorted by residual: dihedral pdb=" C8 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual 173.56 -63.37 -123.07 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O4 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual -63.24 56.71 -119.95 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 185 0.023 - 0.046: 77 0.046 - 0.069: 52 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1773 3.30 - 3.83: 3372 3.83 - 4.37: 3797 4.37 - 4.90: 6913 Nonbonded interactions: 16220 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 3.040 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 3.040 ... (remaining 16215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.440 Find NCS groups from input model: 0.010 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.004 0.118 2226 Z= 0.304 Angle : 0.578 9.250 3019 Z= 0.290 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 18.971 123.074 814 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 PHE 0.002 0.001 PHE A 119 TYR 0.018 0.001 TYR B 113 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.9242 time to fit residues: 58.8484 Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2226 Z= 0.366 Angle : 0.571 4.973 3019 Z= 0.305 Chirality : 0.044 0.141 349 Planarity : 0.004 0.025 383 Dihedral : 8.732 82.158 350 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.49 % Allowed : 31.17 % Favored : 62.34 % 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: 0.19 (0.52), residues: 284 helix: 1.01 (0.74), residues: 51 sheet: 0.36 (0.55), residues: 92 loop : -0.27 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.002 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.256 Fit side-chains REVERT: A 41 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 126 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (ttt180) REVERT: B 47 ARG cc_start: 0.8723 (ttp-170) cc_final: 0.8507 (ttp-170) REVERT: B 75 ASP cc_start: 0.8407 (t0) cc_final: 0.7551 (t70) outliers start: 15 outliers final: 5 residues processed: 49 average time/residue: 1.1087 time to fit residues: 55.6151 Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2226 Z= 0.119 Angle : 0.475 7.503 3019 Z= 0.247 Chirality : 0.041 0.146 349 Planarity : 0.003 0.025 383 Dihedral : 5.231 52.561 347 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 5.63 % Allowed : 31.60 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.52), residues: 284 helix: 1.35 (0.76), residues: 51 sheet: 0.33 (0.51), residues: 97 loop : -0.17 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.003 0.001 PHE A 119 TYR 0.008 0.001 TYR B 118 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.257 Fit side-chains REVERT: A 41 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: B 75 ASP cc_start: 0.8503 (t0) cc_final: 0.8275 (t0) outliers start: 13 outliers final: 5 residues processed: 52 average time/residue: 0.9665 time to fit residues: 51.6056 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.0030 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2226 Z= 0.181 Angle : 0.509 7.162 3019 Z= 0.265 Chirality : 0.042 0.142 349 Planarity : 0.003 0.025 383 Dihedral : 5.107 51.442 346 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.63 % Allowed : 29.00 % Favored : 65.37 % 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: 0.31 (0.51), residues: 284 helix: 1.50 (0.76), residues: 51 sheet: 0.47 (0.54), residues: 77 loop : -0.33 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 82 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.264 Fit side-chains REVERT: A 41 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 75 ASP cc_start: 0.8452 (t0) cc_final: 0.8237 (t0) REVERT: B 103 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7839 (mmp80) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 1.2915 time to fit residues: 60.7227 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2226 Z= 0.281 Angle : 0.570 6.983 3019 Z= 0.292 Chirality : 0.043 0.143 349 Planarity : 0.003 0.026 383 Dihedral : 5.292 50.857 346 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.06 % Allowed : 29.00 % Favored : 64.94 % 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: 0.31 (0.50), residues: 284 helix: 1.47 (0.75), residues: 51 sheet: 0.54 (0.54), residues: 77 loop : -0.35 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.006 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.003 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.251 Fit side-chains REVERT: A 41 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: B 93 THR cc_start: 0.8898 (m) cc_final: 0.8533 (p) outliers start: 14 outliers final: 6 residues processed: 47 average time/residue: 1.0946 time to fit residues: 52.7149 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2226 Z= 0.134 Angle : 0.500 5.522 3019 Z= 0.263 Chirality : 0.041 0.146 349 Planarity : 0.003 0.025 383 Dihedral : 4.913 50.949 346 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.33 % Allowed : 31.17 % Favored : 64.50 % 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: 0.67 (0.52), residues: 284 helix: 1.84 (0.77), residues: 51 sheet: 0.66 (0.54), residues: 82 loop : -0.11 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.003 0.001 PHE A 119 TYR 0.006 0.001 TYR B 96 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.263 Fit side-chains REVERT: A 41 GLU cc_start: 0.8398 (tt0) cc_final: 0.8024 (tt0) REVERT: B 93 THR cc_start: 0.8784 (m) cc_final: 0.8463 (p) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 1.0710 time to fit residues: 49.4552 Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2226 Z= 0.281 Angle : 0.608 7.267 3019 Z= 0.308 Chirality : 0.044 0.134 349 Planarity : 0.003 0.027 383 Dihedral : 5.247 50.484 346 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.19 % Allowed : 30.30 % Favored : 64.50 % 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: 0.48 (0.51), residues: 284 helix: 1.65 (0.75), residues: 51 sheet: 0.67 (0.56), residues: 77 loop : -0.27 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.006 0.001 PHE B 102 TYR 0.007 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.257 Fit side-chains REVERT: A 41 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: B 93 THR cc_start: 0.8825 (m) cc_final: 0.8535 (p) REVERT: B 103 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7747 (mmp80) outliers start: 12 outliers final: 6 residues processed: 45 average time/residue: 1.0995 time to fit residues: 50.6732 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2226 Z= 0.214 Angle : 0.555 6.199 3019 Z= 0.288 Chirality : 0.043 0.137 349 Planarity : 0.003 0.029 383 Dihedral : 5.169 50.665 346 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 32.03 % Favored : 64.07 % 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: 0.54 (0.51), residues: 284 helix: 1.73 (0.75), residues: 51 sheet: 0.74 (0.57), residues: 77 loop : -0.27 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.263 Fit side-chains REVERT: B 93 THR cc_start: 0.8794 (m) cc_final: 0.8520 (p) REVERT: B 103 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7759 (mmp80) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 1.1845 time to fit residues: 52.1378 Evaluate side-chains 44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2226 Z= 0.159 Angle : 0.596 8.626 3019 Z= 0.299 Chirality : 0.042 0.143 349 Planarity : 0.003 0.030 383 Dihedral : 4.855 50.842 346 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.46 % Allowed : 32.90 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.52), residues: 284 helix: 1.94 (0.77), residues: 51 sheet: 0.83 (0.56), residues: 82 loop : -0.12 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.252 Fit side-chains REVERT: A 41 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8061 (tt0) REVERT: B 93 THR cc_start: 0.8745 (m) cc_final: 0.8502 (p) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 1.0187 time to fit residues: 47.0799 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2226 Z= 0.156 Angle : 0.552 5.708 3019 Z= 0.286 Chirality : 0.042 0.137 349 Planarity : 0.004 0.030 383 Dihedral : 4.855 50.440 346 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.03 % Allowed : 33.33 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.52), residues: 284 helix: 2.01 (0.77), residues: 51 sheet: 0.94 (0.56), residues: 82 loop : -0.11 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.006 0.001 TYR B 118 ARG 0.000 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.266 Fit side-chains REVERT: A 41 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8058 (tt0) REVERT: B 93 THR cc_start: 0.8735 (m) cc_final: 0.8501 (p) REVERT: B 103 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7899 (mmp80) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 1.2761 time to fit residues: 53.4980 Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.0570 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.063935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.043674 restraints weight = 6452.671| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 3.15 r_work: 0.2514 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2226 Z= 0.160 Angle : 0.585 8.437 3019 Z= 0.296 Chirality : 0.042 0.179 349 Planarity : 0.003 0.032 383 Dihedral : 4.711 50.332 346 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.03 % Allowed : 34.20 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.53), residues: 284 helix: 2.05 (0.77), residues: 51 sheet: 0.96 (0.57), residues: 82 loop : -0.03 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.000 0.000 HIS A 54 PHE 0.003 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.11 seconds wall clock time: 29 minutes 25.04 seconds (1765.04 seconds total)