null Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hoe-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-2.5-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-2.5-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:09 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-2.5-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 303 and 0 Target number of residues in the AU: 303 Target solvent content: 0.5833 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-2.5-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 57.983 2.464 Wilson plot Bfac: 45.80 14153 reflections ( 97.86 % complete ) and 0 restraints for refining 3372 atoms. Observations/parameters ratio is 1.05 ------------------------------------------------------ Starting model: R = 0.3192 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2231 (Rfree = 0.000) for 3372 atoms. Found 33 (63 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.74 2.81 Round 1: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.463 Round 2: 205 peptides, 21 chains. Longest chain 35 peptides. Score 0.651 Round 3: 231 peptides, 22 chains. Longest chain 40 peptides. Score 0.705 Round 4: 243 peptides, 18 chains. Longest chain 44 peptides. Score 0.772 Round 5: 255 peptides, 20 chains. Longest chain 45 peptides. Score 0.776 Taking the results from Round 5 Chains 21, Residues 235, Estimated correctness of the model 91.1 % 6 chains (137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 198 A 20 chains (237 residues) following loop building 5 chains (139 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 4818 restraints for refining 2853 atoms. 3347 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2708 (Rfree = 0.000) for 2853 atoms. Found 31 (53 requested) and removed 33 (26 requested) atoms. Cycle 2: After refmac, R = 0.2528 (Rfree = 0.000) for 2824 atoms. Found 13 (52 requested) and removed 27 (26 requested) atoms. Cycle 3: After refmac, R = 0.2551 (Rfree = 0.000) for 2790 atoms. Found 13 (51 requested) and removed 27 (26 requested) atoms. Cycle 4: After refmac, R = 0.2424 (Rfree = 0.000) for 2761 atoms. Found 17 (49 requested) and removed 26 (26 requested) atoms. Cycle 5: After refmac, R = 0.2368 (Rfree = 0.000) for 2734 atoms. Found 17 (48 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.73 2.80 Round 1: 256 peptides, 19 chains. Longest chain 43 peptides. Score 0.787 Round 2: 274 peptides, 17 chains. Longest chain 65 peptides. Score 0.832 Round 3: 267 peptides, 19 chains. Longest chain 44 peptides. Score 0.805 Round 4: 270 peptides, 18 chains. Longest chain 42 peptides. Score 0.818 Round 5: 269 peptides, 20 chains. Longest chain 41 peptides. Score 0.800 Taking the results from Round 2 Chains 21, Residues 257, Estimated correctness of the model 94.7 % 7 chains (174 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 125 A Built loop between residues 230 A and 233 A Built loop between residues 355 A and 358 A 16 chains (263 residues) following loop building 4 chains (186 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 4192 restraints for refining 2851 atoms. 2390 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2409 (Rfree = 0.000) for 2851 atoms. Found 26 (48 requested) and removed 34 (26 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 2831 atoms. Found 8 (47 requested) and removed 26 (26 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 2809 atoms. Found 12 (46 requested) and removed 26 (26 requested) atoms. Cycle 9: After refmac, R = 0.2106 (Rfree = 0.000) for 2791 atoms. Found 10 (44 requested) and removed 26 (26 requested) atoms. Cycle 10: After refmac, R = 0.2113 (Rfree = 0.000) for 2766 atoms. Found 15 (43 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.70 2.77 Round 1: 261 peptides, 17 chains. Longest chain 47 peptides. Score 0.812 Round 2: 272 peptides, 14 chains. Longest chain 51 peptides. Score 0.851 Round 3: 270 peptides, 13 chains. Longest chain 48 peptides. Score 0.855 Round 4: 269 peptides, 16 chains. Longest chain 51 peptides. Score 0.832 Round 5: 272 peptides, 15 chains. Longest chain 82 peptides. Score 0.844 Taking the results from Round 3 Chains 17, Residues 257, Estimated correctness of the model 96.0 % 8 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 125 A and 128 A Built loop between residues 144 A and 148 A Built loop between residues 218 A and 224 A 13 chains (264 residues) following loop building 5 chains (215 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3886 restraints for refining 2854 atoms. 2005 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2230 (Rfree = 0.000) for 2854 atoms. Found 25 (42 requested) and removed 32 (26 requested) atoms. Cycle 12: After refmac, R = 0.2043 (Rfree = 0.000) for 2832 atoms. Found 15 (41 requested) and removed 26 (26 requested) atoms. Cycle 13: After refmac, R = 0.1999 (Rfree = 0.000) for 2813 atoms. Found 17 (40 requested) and removed 26 (26 requested) atoms. Cycle 14: After refmac, R = 0.1965 (Rfree = 0.000) for 2796 atoms. Found 11 (38 requested) and removed 26 (26 requested) atoms. Cycle 15: After refmac, R = 0.1932 (Rfree = 0.000) for 2778 atoms. Found 13 (37 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.71 2.78 Round 1: 263 peptides, 19 chains. Longest chain 48 peptides. Score 0.799 Round 2: 265 peptides, 16 chains. Longest chain 47 peptides. Score 0.826 Round 3: 260 peptides, 17 chains. Longest chain 54 peptides. Score 0.811 Round 4: 268 peptides, 15 chains. Longest chain 50 peptides. Score 0.838 Round 5: 271 peptides, 15 chains. Longest chain 82 peptides. Score 0.842 Taking the results from Round 5 Chains 15, Residues 256, Estimated correctness of the model 95.3 % 6 chains (204 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 164 A and 172 A Built loop between residues 355 A and 360 A 13 chains (267 residues) following loop building 4 chains (215 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3977 restraints for refining 2853 atoms. 2084 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2195 (Rfree = 0.000) for 2853 atoms. Found 22 (37 requested) and removed 30 (26 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 2833 atoms. Found 14 (36 requested) and removed 27 (26 requested) atoms. Cycle 18: After refmac, R = 0.1972 (Rfree = 0.000) for 2814 atoms. Found 9 (35 requested) and removed 26 (26 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 2795 atoms. Found 9 (33 requested) and removed 26 (26 requested) atoms. Cycle 20: After refmac, R = 0.1878 (Rfree = 0.000) for 2775 atoms. Found 12 (32 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.71 2.78 Round 1: 260 peptides, 16 chains. Longest chain 47 peptides. Score 0.819 Round 2: 271 peptides, 12 chains. Longest chain 57 peptides. Score 0.863 Round 3: 273 peptides, 15 chains. Longest chain 74 peptides. Score 0.845 Round 4: 273 peptides, 13 chains. Longest chain 96 peptides. Score 0.859 Round 5: 271 peptides, 17 chains. Longest chain 64 peptides. Score 0.827 Taking the results from Round 2 Chains 12, Residues 259, Estimated correctness of the model 96.4 % 7 chains (224 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 182 A Built loop between residues 197 A and 200 A Built loop between residues 221 A and 224 A 9 chains (266 residues) following loop building 4 chains (231 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3709 restraints for refining 2854 atoms. 1722 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 2854 atoms. Found 26 (32 requested) and removed 42 (26 requested) atoms. Cycle 22: After refmac, R = 0.2056 (Rfree = 0.000) for 2832 atoms. Found 14 (31 requested) and removed 29 (26 requested) atoms. Cycle 23: After refmac, R = 0.1967 (Rfree = 0.000) for 2810 atoms. Found 16 (30 requested) and removed 28 (26 requested) atoms. Cycle 24: After refmac, R = 0.1938 (Rfree = 0.000) for 2793 atoms. Found 17 (28 requested) and removed 27 (26 requested) atoms. Cycle 25: After refmac, R = 0.1864 (Rfree = 0.000) for 2778 atoms. Found 15 (27 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.71 2.78 Round 1: 265 peptides, 16 chains. Longest chain 69 peptides. Score 0.826 Round 2: 263 peptides, 11 chains. Longest chain 57 peptides. Score 0.861 Round 3: 264 peptides, 11 chains. Longest chain 70 peptides. Score 0.862 Round 4: 265 peptides, 15 chains. Longest chain 43 peptides. Score 0.834 Round 5: 266 peptides, 16 chains. Longest chain 57 peptides. Score 0.828 Taking the results from Round 3 Chains 13, Residues 253, Estimated correctness of the model 96.3 % 6 chains (213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 A and 149 A Built loop between residues 164 A and 171 A Built loop between residues 220 A and 224 A 9 chains (264 residues) following loop building 3 chains (229 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3711 restraints for refining 2854 atoms. 1759 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2125 (Rfree = 0.000) for 2854 atoms. Found 26 (26 requested) and removed 35 (26 requested) atoms. Cycle 27: After refmac, R = 0.1978 (Rfree = 0.000) for 2839 atoms. Found 13 (26 requested) and removed 26 (26 requested) atoms. Cycle 28: After refmac, R = 0.1930 (Rfree = 0.000) for 2821 atoms. Found 19 (26 requested) and removed 26 (26 requested) atoms. Cycle 29: After refmac, R = 0.1919 (Rfree = 0.000) for 2812 atoms. Found 11 (26 requested) and removed 27 (26 requested) atoms. Cycle 30: After refmac, R = 0.1907 (Rfree = 0.000) for 2791 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.71 2.78 Round 1: 247 peptides, 13 chains. Longest chain 69 peptides. Score 0.823 Round 2: 251 peptides, 11 chains. Longest chain 51 peptides. Score 0.845 Round 3: 263 peptides, 13 chains. Longest chain 40 peptides. Score 0.846 Round 4: 256 peptides, 11 chains. Longest chain 51 peptides. Score 0.852 Round 5: 263 peptides, 14 chains. Longest chain 51 peptides. Score 0.839 Taking the results from Round 4 Chains 11, Residues 245, Estimated correctness of the model 95.8 % 7 chains (209 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 126 A and 129 A Built loop between residues 142 A and 148 A Built loop between residues 164 A and 171 A Built loop between residues 220 A and 228 A 7 chains (265 residues) following loop building 3 chains (229 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3618 restraints for refining 2854 atoms. 1651 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2109 (Rfree = 0.000) for 2854 atoms. Found 20 (26 requested) and removed 34 (26 requested) atoms. Cycle 32: After refmac, R = 0.1960 (Rfree = 0.000) for 2830 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 33: After refmac, R = 0.1905 (Rfree = 0.000) for 2816 atoms. Found 11 (26 requested) and removed 26 (26 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 2797 atoms. Found 14 (26 requested) and removed 27 (26 requested) atoms. Cycle 35: After refmac, R = 0.1861 (Rfree = 0.000) for 2778 atoms. Found 17 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.70 2.77 Round 1: 241 peptides, 15 chains. Longest chain 51 peptides. Score 0.796 Round 2: 254 peptides, 9 chains. Longest chain 67 peptides. Score 0.864 Round 3: 258 peptides, 12 chains. Longest chain 50 peptides. Score 0.847 Round 4: 253 peptides, 10 chains. Longest chain 74 peptides. Score 0.855 Round 5: 253 peptides, 12 chains. Longest chain 59 peptides. Score 0.840 Taking the results from Round 2 Chains 9, Residues 245, Estimated correctness of the model 96.4 % 6 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 147 A Built loop between residues 167 A and 174 A Built loop between residues 220 A and 223 A 6 chains (256 residues) following loop building 3 chains (232 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3745 restraints for refining 2854 atoms. 1807 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 2854 atoms. Found 16 (26 requested) and removed 34 (26 requested) atoms. Cycle 37: After refmac, R = 0.2079 (Rfree = 0.000) for 2829 atoms. Found 9 (26 requested) and removed 29 (26 requested) atoms. Cycle 38: After refmac, R = 0.2029 (Rfree = 0.000) for 2806 atoms. Found 12 (26 requested) and removed 26 (26 requested) atoms. Cycle 39: After refmac, R = 0.1963 (Rfree = 0.000) for 2786 atoms. Found 11 (26 requested) and removed 26 (26 requested) atoms. Cycle 40: After refmac, R = 0.1919 (Rfree = 0.000) for 2769 atoms. Found 14 (26 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.73 2.80 Round 1: 256 peptides, 13 chains. Longest chain 50 peptides. Score 0.837 Round 2: 267 peptides, 11 chains. Longest chain 83 peptides. Score 0.865 Round 3: 257 peptides, 13 chains. Longest chain 67 peptides. Score 0.838 Round 4: 275 peptides, 10 chains. Longest chain 84 peptides. Score 0.881 Round 5: 272 peptides, 14 chains. Longest chain 51 peptides. Score 0.851 Taking the results from Round 4 Chains 10, Residues 265, Estimated correctness of the model 97.2 % 6 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 132 A and 135 A Built loop between residues 168 A and 171 A Built loop between residues 357 A and 360 A 7 chains (271 residues) following loop building 3 chains (245 residues) in sequence following loop building ------------------------------------------------------ 14153 reflections ( 97.86 % complete ) and 3483 restraints for refining 2854 atoms. 1434 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2107 (Rfree = 0.000) for 2854 atoms. Found 20 (26 requested) and removed 36 (26 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 2829 atoms. Found 22 (26 requested) and removed 26 (26 requested) atoms. Cycle 43: After refmac, R = 0.1903 (Rfree = 0.000) for 2817 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 44: After refmac, R = 0.1892 (Rfree = 0.000) for 2801 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.1883 (Rfree = 0.000) for 2783 atoms. Found 16 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.73 2.80 Round 1: 246 peptides, 15 chains. Longest chain 44 peptides. Score 0.805 Round 2: 255 peptides, 12 chains. Longest chain 49 peptides. Score 0.843 Round 3: 255 peptides, 15 chains. Longest chain 46 peptides. Score 0.819 Round 4: 255 peptides, 14 chains. Longest chain 47 peptides. Score 0.827 Round 5: 255 peptides, 13 chains. Longest chain 47 peptides. Score 0.835 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 243, Estimated correctness of the model 95.3 % 7 chains (208 residues) have been docked in sequence Sequence coverage is 85 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 121 A and 128 A Built loop between residues 144 A and 148 A Built loop between residues 164 A and 173 A Built loop between residues 220 A and 223 A 8 chains (259 residues) following loop building 3 chains (227 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14153 reflections ( 97.86 % complete ) and 1918 restraints for refining 1891 atoms. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3300 (Rfree = 0.000) for 1891 atoms. Found 9 (17 requested) and removed 0 (17 requested) atoms. Cycle 47: After refmac, R = 0.3119 (Rfree = 0.000) for 1891 atoms. Found 2 (17 requested) and removed 1 (17 requested) atoms. Cycle 48: After refmac, R = 0.3057 (Rfree = 0.000) for 1891 atoms. Found 1 (17 requested) and removed 0 (17 requested) atoms. Cycle 49: After refmac, R = 0.3020 (Rfree = 0.000) for 1891 atoms. Found 2 (17 requested) and removed 1 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:19:21 GMT 2018 Job finished. TimeTaking 56.36 Used memory is bytes: 10338960