Starting phenix.real_space_refine on Mon Sep 23 15:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/09_2024/8hrm_34978.cif" } resolution = 2.56 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= 0.009 sd= 0.064 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 2224 2.51 5 N 620 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.16, per 1000 atoms: 0.89 Number of scatterers: 3567 At special positions: 0 Unit cell: (68.0021, 57.6201, 62.8111, 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 723 8.00 N 620 7.00 C 2224 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: 0.83 Conformation dependent library (CDL) restraints added in 442.4 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 4.2% alpha, 49.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.589A pdb=" N SER A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.553A pdb=" N SER B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.585A pdb=" N SER C 122 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.601A pdb=" N SER D 122 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.401A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.385A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 23 removed outlier: 5.432A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 23 removed outlier: 5.385A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 480 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: 1.03 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: 1.22 - 1.29: 572 1.29 - 1.35: 584 1.35 - 1.42: 480 1.42 - 1.48: 620 1.48 - 1.55: 1380 Bond restraints: 3636 Sorted by residual: bond pdb=" CB THR D 91 " pdb=" CG2 THR D 91 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CG LEU B 109 " pdb=" CD1 LEU B 109 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" CG LEU A 109 " pdb=" CD1 LEU A 109 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.53e+00 bond pdb=" CB THR B 91 " pdb=" CG2 THR B 91 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.42e+00 bond pdb=" CG LEU C 109 " pdb=" CD1 LEU C 109 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 4820 1.81 - 3.63: 113 3.63 - 5.44: 25 5.44 - 7.25: 12 7.25 - 9.07: 6 Bond angle restraints: 4976 Sorted by residual: angle pdb=" N GLU B 44 " pdb=" CA GLU B 44 " pdb=" C GLU B 44 " ideal model delta sigma weight residual 108.07 113.07 -5.00 1.38e+00 5.25e-01 1.31e+01 angle pdb=" N GLU A 44 " pdb=" CA GLU A 44 " pdb=" C GLU A 44 " ideal model delta sigma weight residual 108.07 112.96 -4.89 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N GLU C 44 " pdb=" CA GLU C 44 " pdb=" C GLU C 44 " ideal model delta sigma weight residual 108.07 112.87 -4.80 1.38e+00 5.25e-01 1.21e+01 angle pdb=" N GLU D 44 " pdb=" CA GLU D 44 " pdb=" C GLU D 44 " ideal model delta sigma weight residual 108.07 112.77 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" C GLU C 44 " pdb=" CA GLU C 44 " pdb=" CB GLU C 44 " ideal model delta sigma weight residual 114.41 106.87 7.54 2.30e+00 1.89e-01 1.08e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.61: 1689 14.61 - 29.23: 208 29.23 - 43.84: 58 43.84 - 58.45: 25 58.45 - 73.06: 4 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA TRP D 79 " pdb=" C TRP D 79 " pdb=" N LYS D 80 " pdb=" CA LYS D 80 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TRP B 79 " pdb=" C TRP B 79 " pdb=" N LYS B 80 " pdb=" CA LYS B 80 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU C 44 " pdb=" C GLU C 44 " pdb=" N SER C 45 " pdb=" CA SER C 45 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 297 0.032 - 0.064: 193 0.064 - 0.096: 32 0.096 - 0.129: 20 0.129 - 0.161: 14 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TRP D 79 " pdb=" N TRP D 79 " pdb=" C TRP D 79 " pdb=" CB TRP D 79 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA TRP B 79 " pdb=" N TRP B 79 " pdb=" C TRP B 79 " pdb=" CB TRP B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 79 " 0.021 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP D 79 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 79 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 79 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 79 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 79 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 79 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 79 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 79 " 0.020 2.00e-02 2.50e+03 1.23e-02 3.76e+00 pdb=" CG TRP B 79 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 79 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 79 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 79 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 79 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 79 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 79 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 79 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 79 " -0.019 2.00e-02 2.50e+03 1.17e-02 3.44e+00 pdb=" CG TRP A 79 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 79 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 79 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 79 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 79 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 79 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 79 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 79 " -0.001 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 161 2.69 - 3.24: 3401 3.24 - 3.80: 6327 3.80 - 4.35: 8100 4.35 - 4.90: 13882 Nonbonded interactions: 31871 Sorted by model distance: nonbonded pdb=" O THR D 57 " pdb=" O HOH D 201 " model vdw 2.138 3.040 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR D 111 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 111 " pdb=" OG SER D 93 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR C 111 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR A 111 " pdb=" OG SER C 93 " model vdw 2.201 3.040 ... (remaining 31866 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' selection = chain 'D' } 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: 0.350 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.005 0.059 3636 Z= 0.332 Angle : 0.817 9.066 4976 Z= 0.424 Chirality : 0.047 0.161 556 Planarity : 0.004 0.053 624 Dihedral : 15.716 73.064 1160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 4.07 % Allowed : 28.78 % Favored : 67.15 % 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: -1.82 (0.38), residues: 468 helix: -3.02 (0.74), residues: 24 sheet: -1.36 (0.28), residues: 284 loop : -0.11 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 79 HIS 0.004 0.002 HIS A 87 PHE 0.011 0.002 PHE C 29 TYR 0.022 0.002 TYR B 54 ARG 0.010 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.355 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.5909 time to fit residues: 50.5852 Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3636 Z= 0.193 Angle : 0.667 5.779 4976 Z= 0.353 Chirality : 0.045 0.145 556 Planarity : 0.004 0.037 624 Dihedral : 5.982 24.064 521 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.77 % Favored : 93.38 % Rotamer: Outliers : 7.56 % Allowed : 22.97 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.38), residues: 468 helix: -2.89 (0.72), residues: 24 sheet: -1.15 (0.27), residues: 288 loop : -0.02 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 79 HIS 0.002 0.001 HIS D 127 PHE 0.007 0.001 PHE C 29 TYR 0.009 0.001 TYR C 54 ARG 0.006 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.378 Fit side-chains REVERT: A 95 GLN cc_start: 0.7994 (pt0) cc_final: 0.7767 (pt0) outliers start: 26 outliers final: 14 residues processed: 86 average time/residue: 0.6438 time to fit residues: 58.5449 Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3636 Z= 0.219 Angle : 0.673 6.191 4976 Z= 0.348 Chirality : 0.044 0.139 556 Planarity : 0.004 0.049 624 Dihedral : 5.909 26.014 519 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.56 % Favored : 94.23 % Rotamer: Outliers : 6.98 % Allowed : 27.03 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.38), residues: 468 helix: -2.56 (0.80), residues: 24 sheet: -0.92 (0.28), residues: 284 loop : -0.13 (0.55), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS A 87 PHE 0.010 0.002 PHE B 29 TYR 0.012 0.001 TYR B 54 ARG 0.012 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 0.374 Fit side-chains REVERT: B 79 TRP cc_start: 0.7068 (m100) cc_final: 0.6836 (m100) REVERT: D 79 TRP cc_start: 0.6965 (m100) cc_final: 0.6374 (m-90) outliers start: 24 outliers final: 15 residues processed: 80 average time/residue: 0.6120 time to fit residues: 52.0776 Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3636 Z= 0.212 Angle : 0.663 6.695 4976 Z= 0.342 Chirality : 0.043 0.140 556 Planarity : 0.003 0.032 624 Dihedral : 6.062 48.963 519 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.69 % Allowed : 29.94 % Favored : 63.37 % 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: -1.33 (0.38), residues: 468 helix: -2.38 (0.84), residues: 24 sheet: -0.88 (0.28), residues: 284 loop : -0.21 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 75 HIS 0.002 0.001 HIS A 87 PHE 0.010 0.002 PHE D 29 TYR 0.009 0.001 TYR B 54 ARG 0.006 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.329 Fit side-chains REVERT: B 79 TRP cc_start: 0.7082 (m100) cc_final: 0.6469 (m-90) REVERT: D 79 TRP cc_start: 0.7012 (m100) cc_final: 0.6402 (m-90) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.6227 time to fit residues: 53.3613 Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 3636 Z= 0.480 Angle : 0.821 7.132 4976 Z= 0.428 Chirality : 0.050 0.157 556 Planarity : 0.004 0.033 624 Dihedral : 7.279 43.601 519 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.91 % Favored : 94.66 % Rotamer: Outliers : 9.30 % Allowed : 28.78 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.37), residues: 468 helix: -2.88 (0.77), residues: 24 sheet: -1.05 (0.28), residues: 280 loop : -0.41 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 75 HIS 0.004 0.002 HIS D 127 PHE 0.013 0.002 PHE C 29 TYR 0.011 0.002 TYR B 54 ARG 0.006 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 66 time to evaluate : 0.350 Fit side-chains REVERT: B 84 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6961 (ptm160) REVERT: D 79 TRP cc_start: 0.6986 (m100) cc_final: 0.6436 (m-90) outliers start: 32 outliers final: 15 residues processed: 89 average time/residue: 0.6784 time to fit residues: 63.4046 Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3636 Z= 0.215 Angle : 0.674 6.305 4976 Z= 0.345 Chirality : 0.045 0.143 556 Planarity : 0.003 0.036 624 Dihedral : 6.998 54.149 519 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 6.40 % Allowed : 30.81 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.36), residues: 468 helix: -2.65 (0.79), residues: 24 sheet: -1.10 (0.27), residues: 280 loop : -0.41 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.001 0.000 HIS A 87 PHE 0.010 0.002 PHE B 29 TYR 0.006 0.001 TYR A 96 ARG 0.009 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 0.369 Fit side-chains REVERT: A 79 TRP cc_start: 0.7099 (m100) cc_final: 0.6632 (m-90) REVERT: A 95 GLN cc_start: 0.8049 (pt0) cc_final: 0.7833 (pt0) REVERT: B 79 TRP cc_start: 0.7091 (m100) cc_final: 0.6393 (m-90) REVERT: B 84 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6968 (ptm160) REVERT: D 79 TRP cc_start: 0.7089 (m100) cc_final: 0.6498 (m-90) REVERT: D 84 ARG cc_start: 0.7037 (ttm110) cc_final: 0.6817 (ptm160) outliers start: 22 outliers final: 14 residues processed: 70 average time/residue: 0.6102 time to fit residues: 45.4062 Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3636 Z= 0.335 Angle : 0.737 5.979 4976 Z= 0.380 Chirality : 0.048 0.164 556 Planarity : 0.003 0.029 624 Dihedral : 6.676 47.465 518 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.27 % Favored : 95.30 % Rotamer: Outliers : 6.69 % Allowed : 30.81 % Favored : 62.50 % 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: -1.76 (0.36), residues: 468 helix: -2.68 (0.78), residues: 24 sheet: -1.15 (0.28), residues: 280 loop : -0.54 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.002 0.001 HIS D 127 PHE 0.013 0.002 PHE B 29 TYR 0.008 0.001 TYR C 54 ARG 0.006 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.362 Fit side-chains REVERT: B 79 TRP cc_start: 0.7061 (m100) cc_final: 0.6383 (m-90) REVERT: B 84 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6947 (ptm160) REVERT: D 79 TRP cc_start: 0.7052 (m100) cc_final: 0.6454 (m-90) REVERT: D 84 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6823 (ptm160) outliers start: 23 outliers final: 11 residues processed: 72 average time/residue: 0.5600 time to fit residues: 42.9790 Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3636 Z= 0.204 Angle : 0.693 7.203 4976 Z= 0.353 Chirality : 0.046 0.157 556 Planarity : 0.003 0.023 624 Dihedral : 5.566 29.169 516 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 5.81 % Allowed : 31.69 % Favored : 62.50 % 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: -1.88 (0.35), residues: 468 helix: -2.30 (0.84), residues: 24 sheet: -1.30 (0.27), residues: 284 loop : -0.52 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 75 HIS 0.001 0.000 HIS D 87 PHE 0.009 0.002 PHE B 29 TYR 0.006 0.001 TYR C 54 ARG 0.007 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.327 Fit side-chains REVERT: A 79 TRP cc_start: 0.7113 (m100) cc_final: 0.6720 (m-90) REVERT: B 79 TRP cc_start: 0.7092 (m100) cc_final: 0.6357 (m-90) REVERT: D 79 TRP cc_start: 0.7088 (m100) cc_final: 0.6481 (m-90) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.5827 time to fit residues: 43.9185 Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 3636 Z= 0.424 Angle : 0.817 8.217 4976 Z= 0.418 Chirality : 0.051 0.171 556 Planarity : 0.004 0.048 624 Dihedral : 6.232 28.921 516 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 4.94 % Allowed : 34.59 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.36), residues: 468 helix: -2.64 (0.78), residues: 24 sheet: -1.23 (0.28), residues: 280 loop : -0.71 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 75 HIS 0.003 0.001 HIS A 127 PHE 0.015 0.002 PHE B 29 TYR 0.014 0.002 TYR D 54 ARG 0.005 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: A 79 TRP cc_start: 0.7086 (m100) cc_final: 0.6383 (m-90) REVERT: B 79 TRP cc_start: 0.7045 (m100) cc_final: 0.6434 (m-90) REVERT: B 84 ARG cc_start: 0.7221 (ptm160) cc_final: 0.6876 (ptm160) REVERT: B 101 GLU cc_start: 0.6921 (pp20) cc_final: 0.6414 (pp20) REVERT: D 79 TRP cc_start: 0.7099 (m100) cc_final: 0.6735 (m-90) REVERT: D 84 ARG cc_start: 0.7094 (ptm160) cc_final: 0.6826 (ptm160) outliers start: 17 outliers final: 13 residues processed: 76 average time/residue: 0.5131 time to fit residues: 41.6643 Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3636 Z= 0.238 Angle : 0.726 7.563 4976 Z= 0.371 Chirality : 0.047 0.158 556 Planarity : 0.003 0.030 624 Dihedral : 5.804 30.850 516 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.94 % Allowed : 34.59 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.35), residues: 468 helix: -2.43 (0.80), residues: 24 sheet: -1.24 (0.27), residues: 280 loop : -0.77 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.001 0.001 HIS B 127 PHE 0.010 0.002 PHE B 29 TYR 0.013 0.001 TYR D 54 ARG 0.003 0.000 ARG C 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.352 Fit side-chains REVERT: A 79 TRP cc_start: 0.7073 (m100) cc_final: 0.6641 (m-90) REVERT: B 79 TRP cc_start: 0.7093 (m100) cc_final: 0.6359 (m-90) REVERT: D 79 TRP cc_start: 0.6970 (m100) cc_final: 0.6601 (m-90) REVERT: D 84 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6752 (ptm160) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.7413 time to fit residues: 54.9716 Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.191135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.164569 restraints weight = 4444.935| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.48 r_work: 0.4004 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 3636 Z= 0.437 Angle : 0.856 7.675 4976 Z= 0.439 Chirality : 0.051 0.160 556 Planarity : 0.005 0.063 624 Dihedral : 6.412 30.157 516 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.36 % Allowed : 35.47 % Favored : 60.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.35), residues: 468 helix: -2.66 (0.78), residues: 24 sheet: -1.26 (0.28), residues: 280 loop : -0.78 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 75 HIS 0.003 0.002 HIS C 127 PHE 0.016 0.003 PHE B 29 TYR 0.012 0.002 TYR D 54 ARG 0.012 0.001 ARG C 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.68 seconds wall clock time: 28 minutes 30.07 seconds (1710.07 seconds total)