Starting phenix.real_space_refine on Thu Dec 7 23:07:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfp_24444/12_2023/7rfp_24444.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 3252 2.51 5 N 1114 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 10, 'TRANS': 107} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Chain: "B" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 10, 'TRANS': 107} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1077 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 288 Chain: "L" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1098 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 369 Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1077 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 288 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1098 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 3.99, per 1000 atoms: 0.72 Number of scatterers: 5532 At special positions: 0 Unit cell: (62.472, 123.848, 168.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1116 8.00 N 1114 7.00 C 3252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS A 60 " distance=2.01 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS B 55 " distance=2.19 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 100 " distance=2.02 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 44 " distance=2.01 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 77 " distance=2.05 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 74 " distance=2.02 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 100 " distance=2.02 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.02 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 218 " distance=2.01 Simple disulfide: pdb=" SG CYS H 238 " - pdb=" SG CYS L 240 " distance=2.08 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 110 " distance=2.04 Simple disulfide: pdb=" SG CYS L 160 " - pdb=" SG CYS L 220 " distance=2.02 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 115 " distance=2.02 Simple disulfide: pdb=" SG CYS I 162 " - pdb=" SG CYS I 218 " distance=2.01 Simple disulfide: pdb=" SG CYS I 238 " - pdb=" SG CYS M 240 " distance=2.08 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 110 " distance=2.05 Simple disulfide: pdb=" SG CYS M 160 " - pdb=" SG CYS M 220 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 7.9% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.586A pdb=" N PHE A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.586A pdb=" N PHE B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'H' and resid 223 through 226 Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.820A pdb=" N GLU L 105 " --> pdb=" O MET L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 153 removed outlier: 3.854A pdb=" N SER L 153 " --> pdb=" O GLU L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 215 removed outlier: 3.944A pdb=" N HIS L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 106 through 110 Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 209 through 211 No H-bonds generated for 'chain 'I' and resid 209 through 211' Processing helix chain 'I' and resid 223 through 226 Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.821A pdb=" N GLU M 105 " --> pdb=" O MET M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 153 removed outlier: 3.854A pdb=" N SER M 153 " --> pdb=" O GLU M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 215 removed outlier: 3.944A pdb=" N HIS M 215 " --> pdb=" O ASP M 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.693A pdb=" N VAL B 140 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 24 through 26 Processing sheet with id=AB2, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.015A pdb=" N MET H 53 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=AB4, first strand: chain 'H' and resid 142 through 146 removed outlier: 5.883A pdb=" N TYR H 198 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 142 through 146 removed outlier: 5.883A pdb=" N TYR H 198 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 173 through 176 Processing sheet with id=AB7, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.346A pdb=" N VAL L 29 " --> pdb=" O THR L 129 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU L 131 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY L 31 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP L 55 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 37 through 41 removed outlier: 3.630A pdb=" N ALA L 93 " --> pdb=" O CYS L 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 140 through 144 removed outlier: 5.637A pdb=" N TYR L 199 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 179 through 181 removed outlier: 4.821A pdb=" N TRP L 174 " --> pdb=" O GLN L 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'I' and resid 30 through 31 removed outlier: 7.140A pdb=" N MET I 53 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR I 69 " --> pdb=" O MET I 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TRP I 55 " --> pdb=" O VAL I 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'I' and resid 142 through 146 removed outlier: 5.883A pdb=" N TYR I 198 " --> pdb=" O ASP I 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 142 through 146 removed outlier: 5.883A pdb=" N TYR I 198 " --> pdb=" O ASP I 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 173 through 176 Processing sheet with id=AC8, first strand: chain 'M' and resid 28 through 30 removed outlier: 6.371A pdb=" N TRP M 55 " --> pdb=" O VAL M 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 37 through 41 Processing sheet with id=AD1, first strand: chain 'M' and resid 140 through 144 removed outlier: 5.636A pdb=" N TYR M 199 " --> pdb=" O ASN M 164 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 179 through 181 removed outlier: 4.820A pdb=" N TRP M 174 " --> pdb=" O GLN M 181 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 726 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: 1.69 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1116 1.26 - 1.41: 1108 1.41 - 1.55: 2955 1.55 - 1.69: 297 1.69 - 1.84: 50 Bond restraints: 5526 Sorted by residual: bond pdb=" C PRO B 143 " pdb=" O PRO B 143 " ideal model delta sigma weight residual 1.235 1.122 0.113 1.30e-02 5.92e+03 7.59e+01 bond pdb=" C PRO A 143 " pdb=" O PRO A 143 " ideal model delta sigma weight residual 1.235 1.126 0.109 1.30e-02 5.92e+03 7.06e+01 bond pdb=" N GLU A 53 " pdb=" CA GLU A 53 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.25e+01 bond pdb=" N ILE A 142 " pdb=" CA ILE A 142 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.70e-03 1.69e+04 1.83e+01 bond pdb=" N ILE M 39 " pdb=" CA ILE M 39 " ideal model delta sigma weight residual 1.458 1.490 -0.033 7.70e-03 1.69e+04 1.80e+01 ... (remaining 5521 not shown) Histogram of bond angle deviations from ideal: 96.62 - 102.95: 25 102.95 - 109.28: 960 109.28 - 115.61: 2244 115.61 - 121.94: 3047 121.94 - 128.27: 1378 Bond angle restraints: 7654 Sorted by residual: angle pdb=" O PRO A 143 " pdb=" C PRO A 143 " pdb=" N GLU A 144 " ideal model delta sigma weight residual 122.64 105.98 16.66 1.35e+00 5.49e-01 1.52e+02 angle pdb=" O PRO B 143 " pdb=" C PRO B 143 " pdb=" N GLU B 144 " ideal model delta sigma weight residual 122.64 106.94 15.70 1.35e+00 5.49e-01 1.35e+02 angle pdb=" C TYR M 113 " pdb=" CA TYR M 113 " pdb=" CB TYR M 113 " ideal model delta sigma weight residual 110.42 96.62 13.80 1.99e+00 2.53e-01 4.81e+01 angle pdb=" O ALA B 49 " pdb=" C ALA B 49 " pdb=" N PRO B 50 " ideal model delta sigma weight residual 121.53 124.64 -3.11 4.60e-01 4.73e+00 4.57e+01 angle pdb=" N ASP M 114 " pdb=" CA ASP M 114 " pdb=" C ASP M 114 " ideal model delta sigma weight residual 111.90 103.06 8.84 1.32e+00 5.74e-01 4.49e+01 ... (remaining 7649 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.23: 3157 13.23 - 26.45: 87 26.45 - 39.67: 18 39.67 - 52.90: 11 52.90 - 66.12: 4 Dihedral angle restraints: 3277 sinusoidal: 121 harmonic: 3156 Sorted by residual: dihedral pdb=" C TYR M 113 " pdb=" N TYR M 113 " pdb=" CA TYR M 113 " pdb=" CB TYR M 113 " ideal model delta harmonic sigma weight residual -122.60 -102.61 -19.99 0 2.50e+00 1.60e-01 6.39e+01 dihedral pdb=" CB CYS B 82 " pdb=" SG CYS B 82 " pdb=" SG CYS B 100 " pdb=" CB CYS B 100 " ideal model delta sinusoidal sigma weight residual 93.00 159.12 -66.12 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 82 " pdb=" SG CYS A 82 " pdb=" SG CYS A 100 " pdb=" CB CYS A 100 " ideal model delta sinusoidal sigma weight residual 93.00 159.11 -66.11 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 3274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 589 0.098 - 0.197: 327 0.197 - 0.295: 92 0.295 - 0.393: 13 0.393 - 0.491: 3 Chirality restraints: 1024 Sorted by residual: chirality pdb=" CA GLU A 66 " pdb=" N GLU A 66 " pdb=" C GLU A 66 " pdb=" CB GLU A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA GLU B 66 " pdb=" N GLU B 66 " pdb=" C GLU B 66 " pdb=" CB GLU B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CA TYR M 113 " pdb=" N TYR M 113 " pdb=" C TYR M 113 " pdb=" CB TYR M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 1021 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 143 " 0.089 2.00e-02 2.50e+03 1.75e-01 3.05e+02 pdb=" C PRO B 143 " -0.301 2.00e-02 2.50e+03 pdb=" O PRO B 143 " 0.132 2.00e-02 2.50e+03 pdb=" N GLU B 144 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 143 " 0.088 2.00e-02 2.50e+03 1.68e-01 2.83e+02 pdb=" C PRO A 143 " -0.289 2.00e-02 2.50e+03 pdb=" O PRO A 143 " 0.127 2.00e-02 2.50e+03 pdb=" N GLU A 144 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 115 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.15e+00 pdb=" C CYS H 115 " -0.052 2.00e-02 2.50e+03 pdb=" O CYS H 115 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA H 116 " 0.017 2.00e-02 2.50e+03 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 1 2.24 - 2.91: 2474 2.91 - 3.57: 6557 3.57 - 4.24: 8969 4.24 - 4.90: 15471 Nonbonded interactions: 33472 Sorted by model distance: nonbonded pdb=" CB THR A 120 " pdb=" O PHE B 125 " model vdw 1.581 3.470 nonbonded pdb=" CB TYR M 113 " pdb=" N ASP M 114 " model vdw 2.275 2.816 nonbonded pdb=" CB SER M 112 " pdb=" N TYR M 113 " model vdw 2.396 2.816 nonbonded pdb=" N TYR L 69 " pdb=" O TYR L 69 " model vdw 2.428 2.496 nonbonded pdb=" N TYR M 69 " pdb=" O TYR M 69 " model vdw 2.428 2.496 ... (remaining 33467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 11.850 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.820 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 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 : 0.014 0.113 5526 Z= 1.053 Angle : 2.065 16.656 7654 Z= 1.455 Chirality : 0.123 0.491 1024 Planarity : 0.009 0.175 1110 Dihedral : 7.118 47.710 1160 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 2.99 % Allowed : 9.53 % Favored : 87.48 % Rotamer: Outliers : 8.00 % Allowed : 4.00 % Favored : 88.00 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 9.09 % 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: -1.46 (0.25), residues: 1102 helix: 0.60 (0.89), residues: 26 sheet: -0.02 (0.25), residues: 413 loop : -1.75 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.664 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.0637 time to fit residues: 3.4233 Evaluate side-chains 16 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0494 time to fit residues: 1.0303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.6532 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5526 Z= 0.288 Angle : 0.765 9.575 7654 Z= 0.450 Chirality : 0.047 0.153 1024 Planarity : 0.004 0.017 1110 Dihedral : 6.528 34.542 1110 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.53 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1102 helix: -1.06 (0.74), residues: 30 sheet: 0.33 (0.26), residues: 397 loop : -0.99 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.645 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0538 time to fit residues: 2.4900 Evaluate side-chains 14 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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: 0.6738 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5526 Z= 0.283 Angle : 0.738 10.597 7654 Z= 0.431 Chirality : 0.046 0.143 1024 Planarity : 0.004 0.018 1110 Dihedral : 6.523 28.895 1110 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.82 % Allowed : 10.98 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.11 (0.26), residues: 1102 helix: -0.06 (0.82), residues: 34 sheet: 0.30 (0.27), residues: 365 loop : -1.42 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.625 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0526 time to fit residues: 2.1853 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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: 0.6652 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5526 Z= 0.128 Angle : 0.542 8.175 7654 Z= 0.316 Chirality : 0.044 0.135 1024 Planarity : 0.002 0.014 1110 Dihedral : 5.215 26.566 1110 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.99 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1102 helix: 0.78 (0.94), residues: 34 sheet: 0.24 (0.27), residues: 383 loop : -1.18 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.624 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0546 time to fit residues: 2.4141 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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: 0.6967 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 5526 Z= 0.529 Angle : 0.992 14.676 7654 Z= 0.590 Chirality : 0.049 0.140 1024 Planarity : 0.006 0.023 1110 Dihedral : 8.638 44.136 1110 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 1.36 % Allowed : 15.15 % Favored : 83.48 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.24), residues: 1102 helix: 0.57 (0.83), residues: 32 sheet: -0.45 (0.27), residues: 357 loop : -2.40 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.636 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0538 time to fit residues: 2.3173 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 0.0770 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 overall best weight: 2.8944 ------------------------------------------------------------------------------- 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: 0.6894 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5526 Z= 0.284 Angle : 0.704 10.327 7654 Z= 0.413 Chirality : 0.046 0.143 1024 Planarity : 0.003 0.018 1110 Dihedral : 7.044 47.031 1110 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.61 % Favored : 86.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1102 helix: 1.33 (0.87), residues: 32 sheet: -0.75 (0.27), residues: 349 loop : -2.48 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.646 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0561 time to fit residues: 2.4005 Evaluate side-chains 14 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5526 Z= 0.430 Angle : 0.862 12.146 7654 Z= 0.511 Chirality : 0.047 0.165 1024 Planarity : 0.005 0.022 1110 Dihedral : 8.138 46.308 1110 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 18.51 % Favored : 80.85 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.35 (0.23), residues: 1102 helix: 0.69 (0.81), residues: 32 sheet: -1.45 (0.26), residues: 353 loop : -2.96 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0541 time to fit residues: 2.3460 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.7063 moved from start: 0.8712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5526 Z= 0.544 Angle : 0.986 14.597 7654 Z= 0.586 Chirality : 0.050 0.191 1024 Planarity : 0.006 0.029 1110 Dihedral : 9.078 49.139 1110 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.82 % Allowed : 22.05 % Favored : 77.13 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -4.23 (0.22), residues: 1102 helix: 0.43 (0.86), residues: 32 sheet: -2.07 (0.26), residues: 343 loop : -3.57 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.658 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0529 time to fit residues: 2.2464 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.0970 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5526 Z= 0.362 Angle : 0.796 12.657 7654 Z= 0.468 Chirality : 0.046 0.150 1024 Planarity : 0.004 0.023 1110 Dihedral : 7.890 40.671 1110 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.64 % Allowed : 20.15 % Favored : 79.22 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -4.11 (0.23), residues: 1102 helix: 0.73 (0.90), residues: 32 sheet: -2.00 (0.27), residues: 334 loop : -3.49 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.698 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0554 time to fit residues: 2.3174 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.9118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5526 Z= 0.487 Angle : 0.933 13.183 7654 Z= 0.552 Chirality : 0.048 0.185 1024 Planarity : 0.005 0.027 1110 Dihedral : 8.807 44.980 1110 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.82 % Allowed : 24.05 % Favored : 75.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.53 (0.22), residues: 1102 helix: 0.51 (0.89), residues: 32 sheet: -2.33 (0.27), residues: 310 loop : -3.74 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.683 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0519 time to fit residues: 2.2001 Evaluate side-chains 13 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.084917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073087 restraints weight = 27753.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072389 restraints weight = 38178.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072439 restraints weight = 39710.671| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5526 Z= 0.197 Angle : 0.634 9.854 7654 Z= 0.370 Chirality : 0.045 0.143 1024 Planarity : 0.003 0.013 1110 Dihedral : 6.704 34.668 1110 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.88 % Favored : 84.57 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.98 (0.23), residues: 1102 helix: 1.23 (0.93), residues: 32 sheet: -1.92 (0.28), residues: 324 loop : -3.41 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 119 PHE 0.000 0.000 PHE A 96 TYR 0.000 0.000 TYR A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1109.33 seconds wall clock time: 20 minutes 27.78 seconds (1227.78 seconds total)