Starting phenix.real_space_refine on Fri Dec 27 04:09:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4a_31705/12_2024/7v4a_31705.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 1029 2.51 5 N 294 2.21 5 O 330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 1653 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 551 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, B Time building chain proxies: 1.11, per 1000 atoms: 0.67 Number of scatterers: 1653 At special positions: 0 Unit cell: (67.84, 86.92, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 330 8.00 N 294 7.00 C 1029 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: 0.94 Conformation dependent library (CDL) restraints added in 228.7 milliseconds 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.702A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.620A pdb=" N THR A 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.604A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.744A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.729A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 91 30 hydrogen bonds defined for protein. 90 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: 0.35 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 291 1.29 - 1.36: 258 1.36 - 1.42: 51 1.42 - 1.48: 270 1.48 - 1.55: 786 Bond restraints: 1656 Sorted by residual: bond pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.63e-02 3.76e+03 9.11e-01 bond pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.63e-02 3.76e+03 8.64e-01 bond pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.63e-02 3.76e+03 7.79e-01 bond pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 1.516 1.502 0.014 2.50e-02 1.60e+03 3.35e-01 bond pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.08e-02 8.57e+03 3.27e-01 ... (remaining 1651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 2047 0.89 - 1.79: 155 1.79 - 2.68: 12 2.68 - 3.58: 6 3.58 - 4.47: 3 Bond angle restraints: 2223 Sorted by residual: angle pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 5.00e+00 angle pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 4.99e+00 angle pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 angle pdb=" C GLU C 83 " pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 110.44 107.32 3.12 1.68e+00 3.54e-01 3.46e+00 angle pdb=" C GLU A 83 " pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 110.44 107.33 3.11 1.68e+00 3.54e-01 3.44e+00 ... (remaining 2218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 912 17.48 - 34.95: 45 34.95 - 52.42: 15 52.42 - 69.89: 3 69.89 - 87.37: 3 Dihedral angle restraints: 978 sinusoidal: 339 harmonic: 639 Sorted by residual: dihedral pdb=" CB GLU B 20 " pdb=" CG GLU B 20 " pdb=" CD GLU B 20 " pdb=" OE1 GLU B 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.37 -87.37 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU C 20 " pdb=" CG GLU C 20 " pdb=" CD GLU C 20 " pdb=" OE1 GLU C 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.36 -87.36 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 20 " pdb=" CG GLU A 20 " pdb=" CD GLU A 20 " pdb=" OE1 GLU A 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.32 -87.32 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 134 0.026 - 0.052: 81 0.052 - 0.077: 22 0.077 - 0.103: 25 0.103 - 0.128: 23 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA VAL C 15 " pdb=" N VAL C 15 " pdb=" C VAL C 15 " pdb=" CB VAL C 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 282 not shown) Planarity restraints: 276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 83 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" CD GLU C 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU C 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU A 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU B 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU B 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 83 " 0.011 2.00e-02 2.50e+03 ... (remaining 273 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 667 2.92 - 3.41: 1441 3.41 - 3.91: 2358 3.91 - 4.40: 2385 4.40 - 4.90: 5063 Nonbonded interactions: 11914 Sorted by model distance: nonbonded pdb=" N ASP A 98 " pdb=" OD1 ASP A 98 " model vdw 2.423 3.120 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.423 3.120 nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.424 3.120 nonbonded pdb=" N GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.444 3.120 nonbonded pdb=" N GLU B 83 " pdb=" OE1 GLU B 83 " model vdw 2.445 3.120 ... (remaining 11909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.010 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.016 1656 Z= 0.152 Angle : 0.518 4.471 2223 Z= 0.314 Chirality : 0.052 0.128 285 Planarity : 0.002 0.018 276 Dihedral : 14.278 87.365 576 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: -5.80 (0.26), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.20), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.001 0.000 PHE C 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.186 Fit side-chains REVERT: A 21 LYS cc_start: 0.9387 (tttm) cc_final: 0.9148 (tttt) REVERT: A 58 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7898 (tptp) REVERT: A 60 LYS cc_start: 0.8623 (mmtp) cc_final: 0.7923 (mttp) REVERT: A 80 LYS cc_start: 0.8612 (mttp) cc_final: 0.7335 (pttp) REVERT: A 97 LYS cc_start: 0.8710 (ptmm) cc_final: 0.7552 (tppt) REVERT: B 20 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 46 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 58 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8094 (tppt) REVERT: B 59 THR cc_start: 0.9172 (m) cc_final: 0.8882 (t) REVERT: B 60 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7959 (mmtm) REVERT: C 23 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8426 (mmmt) REVERT: C 45 LYS cc_start: 0.8431 (tttp) cc_final: 0.8186 (ttpt) REVERT: C 46 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 58 LYS cc_start: 0.8656 (ttmm) cc_final: 0.7995 (pttm) REVERT: C 60 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7750 (mttm) REVERT: C 61 GLU cc_start: 0.8071 (mp0) cc_final: 0.7596 (mp0) REVERT: C 80 LYS cc_start: 0.8339 (mttp) cc_final: 0.7649 (mmtt) REVERT: C 83 GLU cc_start: 0.5457 (mp0) cc_final: 0.4921 (mp0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2042 time to fit residues: 15.8744 Evaluate side-chains 58 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 1656 Z= 0.438 Angle : 0.608 3.796 2223 Z= 0.360 Chirality : 0.051 0.132 285 Planarity : 0.003 0.011 276 Dihedral : 5.660 19.677 237 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 4.85 % Allowed : 21.21 % Favored : 73.94 % 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: -5.34 (0.30), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.23), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE B 94 TYR 0.015 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.189 Fit side-chains REVERT: A 24 GLN cc_start: 0.8857 (mm110) cc_final: 0.8396 (mp10) REVERT: A 58 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8140 (tptp) REVERT: A 60 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8214 (mttp) REVERT: A 80 LYS cc_start: 0.8806 (mttp) cc_final: 0.7547 (pttp) REVERT: A 97 LYS cc_start: 0.8895 (ptmm) cc_final: 0.7514 (tppt) REVERT: B 20 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 46 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7018 (tm-30) REVERT: C 23 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8510 (mmmt) REVERT: C 45 LYS cc_start: 0.8418 (tttp) cc_final: 0.8205 (ttpt) REVERT: C 46 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7097 (tm-30) REVERT: C 58 LYS cc_start: 0.8506 (ttmm) cc_final: 0.7903 (pttm) REVERT: C 60 LYS cc_start: 0.8619 (mmtp) cc_final: 0.6576 (pttm) REVERT: C 61 GLU cc_start: 0.8169 (mp0) cc_final: 0.7726 (mp0) REVERT: C 80 LYS cc_start: 0.8723 (mttp) cc_final: 0.8051 (mmtt) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1817 time to fit residues: 12.6069 Evaluate side-chains 62 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1656 Z= 0.107 Angle : 0.424 2.701 2223 Z= 0.250 Chirality : 0.049 0.123 285 Planarity : 0.001 0.007 276 Dihedral : 4.130 14.674 237 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.64 % Allowed : 21.21 % Favored : 75.15 % 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: -4.82 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.000 PHE A 94 TYR 0.008 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.201 Fit side-chains REVERT: A 58 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7947 (tptp) REVERT: A 97 LYS cc_start: 0.8802 (ptmm) cc_final: 0.7489 (tppt) REVERT: B 46 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 83 GLU cc_start: 0.5943 (mp0) cc_final: 0.5611 (mp0) REVERT: C 23 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8497 (mmmt) REVERT: C 46 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 58 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7974 (pttm) REVERT: C 60 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8064 (mmtm) REVERT: C 61 GLU cc_start: 0.7993 (mp0) cc_final: 0.7634 (mp0) REVERT: C 80 LYS cc_start: 0.8568 (mttp) cc_final: 0.7905 (mmtt) outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.1798 time to fit residues: 11.5765 Evaluate side-chains 54 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1656 Z= 0.312 Angle : 0.517 3.396 2223 Z= 0.305 Chirality : 0.050 0.126 285 Planarity : 0.002 0.014 276 Dihedral : 4.886 14.960 237 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.48 % Allowed : 18.18 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE B 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.185 Fit side-chains REVERT: A 58 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7961 (tptt) REVERT: A 80 LYS cc_start: 0.8810 (mttp) cc_final: 0.7570 (pttp) REVERT: A 97 LYS cc_start: 0.8844 (ptmm) cc_final: 0.7493 (tppt) REVERT: B 46 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7053 (tm-30) REVERT: C 23 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8499 (mmmt) REVERT: C 46 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 58 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7905 (pttm) REVERT: C 60 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8083 (mmtm) REVERT: C 61 GLU cc_start: 0.8103 (mp0) cc_final: 0.7660 (mp0) REVERT: C 80 LYS cc_start: 0.8705 (mttp) cc_final: 0.7958 (mmtt) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.1622 time to fit residues: 11.2703 Evaluate side-chains 64 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1656 Z= 0.253 Angle : 0.491 3.047 2223 Z= 0.290 Chirality : 0.049 0.128 285 Planarity : 0.002 0.008 276 Dihedral : 4.794 14.948 237 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 7.88 % Allowed : 20.00 % Favored : 72.12 % 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: -4.68 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.191 Fit side-chains REVERT: A 24 GLN cc_start: 0.8467 (mp10) cc_final: 0.8033 (mp10) REVERT: A 58 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7921 (tptt) REVERT: A 61 GLU cc_start: 0.8200 (mp0) cc_final: 0.7995 (mp0) REVERT: A 80 LYS cc_start: 0.8768 (mttp) cc_final: 0.7547 (pttp) REVERT: A 97 LYS cc_start: 0.8813 (ptmm) cc_final: 0.7482 (tppt) REVERT: B 46 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 23 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8488 (mmmt) REVERT: C 46 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7220 (tm-30) REVERT: C 58 LYS cc_start: 0.8575 (ttmm) cc_final: 0.7967 (pttm) REVERT: C 60 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8060 (mmtm) REVERT: C 61 GLU cc_start: 0.8098 (mp0) cc_final: 0.7674 (mp0) REVERT: C 80 LYS cc_start: 0.8693 (mttp) cc_final: 0.7984 (mmtt) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.1762 time to fit residues: 11.6643 Evaluate side-chains 63 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.0010 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1656 Z= 0.289 Angle : 0.502 3.277 2223 Z= 0.297 Chirality : 0.050 0.128 285 Planarity : 0.002 0.008 276 Dihedral : 4.933 15.127 237 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 9.09 % Allowed : 19.39 % Favored : 71.52 % 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: -4.59 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.234 Fit side-chains REVERT: A 24 GLN cc_start: 0.8467 (mp10) cc_final: 0.8107 (mp10) REVERT: A 58 LYS cc_start: 0.8438 (ttmm) cc_final: 0.7927 (tptt) REVERT: A 61 GLU cc_start: 0.8211 (mp0) cc_final: 0.7930 (mp0) REVERT: A 80 LYS cc_start: 0.8795 (mttp) cc_final: 0.7573 (pttp) REVERT: A 97 LYS cc_start: 0.8832 (ptmm) cc_final: 0.7485 (tppt) REVERT: B 46 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 23 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8494 (mmmt) REVERT: C 46 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 58 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7969 (pttm) REVERT: C 60 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8080 (mmtm) REVERT: C 61 GLU cc_start: 0.8111 (mp0) cc_final: 0.7678 (mp0) REVERT: C 80 LYS cc_start: 0.8719 (mttp) cc_final: 0.8015 (mmtt) outliers start: 15 outliers final: 13 residues processed: 64 average time/residue: 0.1699 time to fit residues: 12.0681 Evaluate side-chains 66 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 1656 Z= 0.464 Angle : 0.623 4.504 2223 Z= 0.366 Chirality : 0.052 0.133 285 Planarity : 0.002 0.011 276 Dihedral : 5.559 17.916 237 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 9.70 % Allowed : 18.79 % Favored : 71.52 % 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: -4.66 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.006 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.180 Fit side-chains REVERT: A 24 GLN cc_start: 0.8492 (mp10) cc_final: 0.8094 (mp10) REVERT: A 58 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8049 (tptp) REVERT: A 80 LYS cc_start: 0.8824 (mttp) cc_final: 0.7715 (pttp) REVERT: A 97 LYS cc_start: 0.8799 (ptmm) cc_final: 0.7481 (tppt) REVERT: B 46 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6943 (tm-30) REVERT: C 23 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8497 (mmmt) REVERT: C 46 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 57 GLU cc_start: 0.3909 (pm20) cc_final: 0.3646 (pm20) REVERT: C 58 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7776 (pttm) REVERT: C 60 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8059 (mmtm) REVERT: C 61 GLU cc_start: 0.8168 (mp0) cc_final: 0.7758 (mp0) REVERT: C 80 LYS cc_start: 0.8796 (mttp) cc_final: 0.8049 (mmtt) outliers start: 16 outliers final: 14 residues processed: 64 average time/residue: 0.1674 time to fit residues: 11.8902 Evaluate side-chains 66 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.0270 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.0030 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.4448 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1656 Z= 0.107 Angle : 0.415 2.720 2223 Z= 0.245 Chirality : 0.049 0.132 285 Planarity : 0.002 0.009 276 Dihedral : 4.316 15.103 237 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.03 % Allowed : 25.45 % Favored : 71.52 % 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: -4.24 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE A 94 TYR 0.015 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.245 Fit side-chains REVERT: A 24 GLN cc_start: 0.8459 (mp10) cc_final: 0.8117 (mp10) REVERT: A 58 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7978 (tptp) REVERT: A 97 LYS cc_start: 0.8776 (ptmm) cc_final: 0.7503 (tppt) REVERT: B 46 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6821 (tm-30) REVERT: B 57 GLU cc_start: 0.8101 (pm20) cc_final: 0.7617 (pm20) REVERT: C 23 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8490 (mmmt) REVERT: C 46 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 58 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7911 (pttm) REVERT: C 60 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8016 (mmtm) REVERT: C 61 GLU cc_start: 0.8063 (mp0) cc_final: 0.7657 (mp0) REVERT: C 80 LYS cc_start: 0.8631 (mttp) cc_final: 0.7898 (mmtt) REVERT: C 97 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8376 (ptmt) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.1852 time to fit residues: 11.9314 Evaluate side-chains 57 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0170 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 1.1020 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1656 Z= 0.162 Angle : 0.462 4.710 2223 Z= 0.270 Chirality : 0.049 0.127 285 Planarity : 0.002 0.020 276 Dihedral : 4.405 14.633 237 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.64 % Allowed : 25.45 % Favored : 70.91 % 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: -4.18 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.225 Fit side-chains REVERT: A 24 GLN cc_start: 0.8452 (mp10) cc_final: 0.8105 (mp10) REVERT: B 46 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6968 (tm-30) REVERT: C 23 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8484 (mmmt) REVERT: C 46 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7188 (tm-30) REVERT: C 58 LYS cc_start: 0.8535 (ttmm) cc_final: 0.7892 (pttm) REVERT: C 60 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8000 (mmtm) REVERT: C 61 GLU cc_start: 0.8086 (mp0) cc_final: 0.7669 (mp0) REVERT: C 80 LYS cc_start: 0.8672 (mttp) cc_final: 0.7941 (mmtt) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1413 time to fit residues: 8.7043 Evaluate side-chains 55 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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: 0.7984 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1656 Z= 0.188 Angle : 0.507 8.061 2223 Z= 0.294 Chirality : 0.049 0.127 285 Planarity : 0.002 0.015 276 Dihedral : 4.501 14.617 237 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 4.85 % Allowed : 25.45 % Favored : 69.70 % 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: -4.16 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.190 Fit side-chains REVERT: A 24 GLN cc_start: 0.8434 (mp10) cc_final: 0.8105 (mp10) REVERT: B 46 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6893 (tm-30) REVERT: B 57 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: C 23 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8483 (mmmt) REVERT: C 46 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7138 (tm-30) REVERT: C 58 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7938 (pttm) REVERT: C 60 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8050 (mmtm) REVERT: C 61 GLU cc_start: 0.8093 (mp0) cc_final: 0.7669 (mp0) REVERT: C 80 LYS cc_start: 0.8683 (mttp) cc_final: 0.7952 (mmtt) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.1364 time to fit residues: 8.6701 Evaluate side-chains 58 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.137223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108975 restraints weight = 2234.978| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.37 r_work: 0.3557 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1656 Z= 0.297 Angle : 0.559 7.707 2223 Z= 0.327 Chirality : 0.050 0.129 285 Planarity : 0.002 0.015 276 Dihedral : 4.930 14.925 237 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 6.06 % Allowed : 24.85 % Favored : 69.09 % 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: -4.26 (0.37), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.29), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.09 seconds wall clock time: 20 minutes 38.93 seconds (1238.93 seconds total)