Tue 25 Dec 19:27:55 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 1vk4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.2-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/1vk4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.2-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 ============================================================ Tue 25 Dec 19:28:05 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/1vk4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.2-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 212 and 0 Target number of residues in the AU: 212 Target solvent content: 0.5976 Checking the provided sequence file Detected sequence length: 298 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 298 Adjusted target solvent content: 0.43 Input MTZ file: 1vk4-3.2-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: 19 Cell parameters: 43.308 68.545 96.054 90.000 90.000 90.000 Input sequence file: 1vk4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2384 target number of atoms Had to go as low as 0.55 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: 55.795 3.200 Wilson plot Bfac: 51.43 5030 reflections ( 99.37 % complete ) and 0 restraints for refining 2650 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.2971 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2435 (Rfree = 0.000) for 2650 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 3.32 Search for helices and strands: 0 residues in 0 chains, 2698 seeds are put forward Round 1: 149 peptides, 29 chains. Longest chain 10 peptides. Score 0.366 Round 2: 189 peptides, 29 chains. Longest chain 15 peptides. Score 0.565 Round 3: 188 peptides, 22 chains. Longest chain 19 peptides. Score 0.681 Round 4: 201 peptides, 21 chains. Longest chain 24 peptides. Score 0.736 Round 5: 214 peptides, 23 chains. Longest chain 22 peptides. Score 0.746 Taking the results from Round 5 Chains 27, Residues 191, Estimated correctness of the model 74.3 % 2 chains (26 residues) have been docked in sequence Building loops using Loopy2018 27 chains (191 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ 5030 reflections ( 99.37 % complete ) and 4230 restraints for refining 2173 atoms. 3391 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2548 (Rfree = 0.000) for 2173 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2310 (Rfree = 0.000) for 2138 atoms. Found 12 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2298 (Rfree = 0.000) for 2120 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2114 (Rfree = 0.000) for 2111 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2086 (Rfree = 0.000) for 2103 atoms. Found 4 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 2174 seeds are put forward Round 1: 187 peptides, 19 chains. Longest chain 27 peptides. Score 0.722 Round 2: 203 peptides, 23 chains. Longest chain 30 peptides. Score 0.714 Round 3: 214 peptides, 18 chains. Longest chain 32 peptides. Score 0.804 Round 4: 213 peptides, 20 chains. Longest chain 31 peptides. Score 0.780 Round 5: 210 peptides, 16 chains. Longest chain 38 peptides. Score 0.817 Taking the results from Round 5 Chains 18, Residues 194, Estimated correctness of the model 85.9 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 18 chains (194 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ 5030 reflections ( 99.37 % complete ) and 4108 restraints for refining 2177 atoms. 3123 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2520 (Rfree = 0.000) for 2177 atoms. Found 17 (17 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2181 (Rfree = 0.000) for 2161 atoms. Found 14 (17 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2112 (Rfree = 0.000) for 2162 atoms. Found 4 (16 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2014 (Rfree = 0.000) for 2150 atoms. Found 5 (16 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1945 (Rfree = 0.000) for 2141 atoms. Found 3 (16 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.93 3.22 Search for helices and strands: 0 residues in 0 chains, 2217 seeds are put forward Round 1: 194 peptides, 19 chains. Longest chain 30 peptides. Score 0.743 Round 2: 210 peptides, 20 chains. Longest chain 30 peptides. Score 0.772 Round 3: 220 peptides, 20 chains. Longest chain 38 peptides. Score 0.796 Round 4: 221 peptides, 19 chains. Longest chain 27 peptides. Score 0.808 Round 5: 217 peptides, 20 chains. Longest chain 31 peptides. Score 0.789 Taking the results from Round 4 Chains 21, Residues 202, Estimated correctness of the model 84.6 % 3 chains (62 residues) have been docked in sequence Building loops using Loopy2018 21 chains (202 residues) following loop building 3 chains (62 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5030 reflections ( 99.37 % complete ) and 4019 restraints for refining 2177 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2769 (Rfree = 0.000) for 2177 atoms. Found 15 (15 requested) and removed 19 (9 requested) atoms. Cycle 12: After refmac, R = 0.2347 (Rfree = 0.000) for 2159 atoms. Found 8 (15 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.2255 (Rfree = 0.000) for 2151 atoms. Found 8 (14 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2398 (Rfree = 0.000) for 2145 atoms. Found 14 (14 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.2475 (Rfree = 0.000) for 2140 atoms. Found 14 (14 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 2220 seeds are put forward Round 1: 202 peptides, 21 chains. Longest chain 23 peptides. Score 0.739 Round 2: 214 peptides, 19 chains. Longest chain 27 peptides. Score 0.793 Round 3: 211 peptides, 17 chains. Longest chain 28 peptides. Score 0.808 Round 4: 212 peptides, 17 chains. Longest chain 36 peptides. Score 0.810 Round 5: 215 peptides, 19 chains. Longest chain 36 peptides. Score 0.795 Taking the results from Round 4 Chains 21, Residues 195, Estimated correctness of the model 84.9 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 21 chains (195 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ 5030 reflections ( 99.37 % complete ) and 4181 restraints for refining 2177 atoms. 3216 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 2177 atoms. Found 13 (13 requested) and removed 17 (9 requested) atoms. Cycle 17: After refmac, R = 0.2131 (Rfree = 0.000) for 2167 atoms. Found 5 (13 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2029 (Rfree = 0.000) for 2158 atoms. Found 7 (13 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1876 (Rfree = 0.000) for 2153 atoms. Found 2 (12 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1768 (Rfree = 0.000) for 2143 atoms. Found 5 (12 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward Round 1: 186 peptides, 24 chains. Longest chain 18 peptides. Score 0.641 Round 2: 205 peptides, 18 chains. Longest chain 31 peptides. Score 0.784 Round 3: 211 peptides, 17 chains. Longest chain 32 peptides. Score 0.808 Round 4: 222 peptides, 22 chains. Longest chain 26 peptides. Score 0.778 Round 5: 208 peptides, 20 chains. Longest chain 22 peptides. Score 0.767 Taking the results from Round 3 Chains 17, Residues 194, Estimated correctness of the model 84.6 % 2 chains (49 residues) have been docked in sequence Building loops using Loopy2018 17 chains (194 residues) following loop building 2 chains (49 residues) in sequence following loop building ------------------------------------------------------ 5030 reflections ( 99.37 % complete ) and 4216 restraints for refining 2177 atoms. 3259 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2191 (Rfree = 0.000) for 2177 atoms. Found 11 (11 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1952 (Rfree = 0.000) for 2165 atoms. Found 8 (11 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.1873 (Rfree = 0.000) for 2156 atoms. Found 10 (11 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2247 (Rfree = 0.000) for 2148 atoms. Found 10 (10 requested) and removed 14 (9 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2242 (Rfree = 0.000) for 2136 atoms. Found 10 (10 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.93 3.22 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward Round 1: 188 peptides, 19 chains. Longest chain 21 peptides. Score 0.725 Round 2: 205 peptides, 15 chains. Longest chain 27 peptides. Score 0.817 Round 3: 202 peptides, 21 chains. Longest chain 24 peptides. Score 0.739 Round 4: 207 peptides, 16 chains. Longest chain 29 peptides. Score 0.810 Round 5: 192 peptides, 21 chains. Longest chain 21 peptides. Score 0.709 Taking the results from Round 2 Chains 21, Residues 190, Estimated correctness of the model 85.9 % 5 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 93 A 20 chains (189 residues) following loop building 4 chains (90 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5030 reflections ( 99.37 % complete ) and 3662 restraints for refining 2164 atoms. 2610 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2280 (Rfree = 0.000) for 2164 atoms. Found 9 (9 requested) and removed 24 (9 requested) atoms. Cycle 27: After refmac, R = 0.2060 (Rfree = 0.000) for 2145 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.1961 (Rfree = 0.000) for 2141 atoms. Found 9 (9 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2053 (Rfree = 0.000) for 2137 atoms. Found 9 (9 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1901 (Rfree = 0.000) for 2130 atoms. Found 7 (9 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 3.27 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward Round 1: 169 peptides, 21 chains. Longest chain 28 peptides. Score 0.628 Round 2: 196 peptides, 19 chains. Longest chain 30 peptides. Score 0.748 Round 3: 182 peptides, 21 chains. Longest chain 17 peptides. Score 0.676 Round 4: 180 peptides, 17 chains. Longest chain 26 peptides. Score 0.729 Round 5: 175 peptides, 20 chains. Longest chain 17 peptides. Score 0.667 Taking the results from Round 2 Chains 20, Residues 177, Estimated correctness of the model 74.7 % 3 chains (61 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 159 A and 165 A 19 chains (181 residues) following loop building 2 chains (66 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5030 reflections ( 99.37 % complete ) and 3919 restraints for refining 2177 atoms. 2938 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2417 (Rfree = 0.000) for 2177 atoms. Found 9 (9 requested) and removed 14 (9 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2152 (Rfree = 0.000) for 2167 atoms. Found 8 (9 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2025 (Rfree = 0.000) for 2159 atoms. Found 5 (9 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2072 (Rfree = 0.000) for 2151 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1847 (Rfree = 0.000) for 2149 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 3.32 Search for helices and strands: 0 residues in 0 chains, 2213 seeds are put forward Round 1: 165 peptides, 20 chains. Longest chain 21 peptides. Score 0.630 Round 2: 187 peptides, 21 chains. Longest chain 24 peptides. Score 0.693 Round 3: 191 peptides, 20 chains. Longest chain 25 peptides. Score 0.720 Round 4: 183 peptides, 25 chains. Longest chain 15 peptides. Score 0.613 Round 5: 186 peptides, 23 chains. Longest chain 21 peptides. Score 0.658 Taking the results from Round 3 Chains 20, Residues 171, Estimated correctness of the model 69.3 % 3 chains (61 residues) have been docked in sequence Building loops using Loopy2018 20 chains (171 residues) following loop building 3 chains (61 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5030 reflections ( 99.37 % complete ) and 4124 restraints for refining 2177 atoms. 3200 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2245 (Rfree = 0.000) for 2177 atoms. Found 9 (9 requested) and removed 15 (9 requested) atoms. Cycle 37: After refmac, R = 0.1954 (Rfree = 0.000) for 2168 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.1830 (Rfree = 0.000) for 2160 atoms. Found 7 (9 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1791 (Rfree = 0.000) for 2158 atoms. Found 1 (9 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1777 (Rfree = 0.000) for 2150 atoms. Found 3 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.94 3.23 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward Round 1: 156 peptides, 21 chains. Longest chain 17 peptides. Score 0.574 Round 2: 174 peptides, 20 chains. Longest chain 25 peptides. Score 0.664 Round 3: 171 peptides, 19 chains. Longest chain 20 peptides. Score 0.669 Round 4: 175 peptides, 20 chains. Longest chain 27 peptides. Score 0.667 Round 5: 167 peptides, 20 chains. Longest chain 21 peptides. Score 0.638 Taking the results from Round 3 Chains 19, Residues 152, Estimated correctness of the model 58.3 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5030 reflections ( 99.37 % complete ) and 4565 restraints for refining 2177 atoms. 3831 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1901 (Rfree = 0.000) for 2177 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.1776 (Rfree = 0.000) for 2176 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 2175 atoms. Found 3 (9 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.1679 (Rfree = 0.000) for 2167 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1668 (Rfree = 0.000) for 2164 atoms. Found 4 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.02 3.32 Search for helices and strands: 0 residues in 0 chains, 2225 seeds are put forward Round 1: 169 peptides, 20 chains. Longest chain 23 peptides. Score 0.645 Round 2: 179 peptides, 20 chains. Longest chain 27 peptides. Score 0.681 Round 3: 176 peptides, 19 chains. Longest chain 22 peptides. Score 0.687 Round 4: 174 peptides, 15 chains. Longest chain 28 peptides. Score 0.740 Round 5: 173 peptides, 19 chains. Longest chain 22 peptides. Score 0.676 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 159, Estimated correctness of the model 73.2 % 3 chains (67 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 1vk4-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (159 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5030 reflections ( 99.37 % complete ) and 4093 restraints for refining 2177 atoms. 3184 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1998 (Rfree = 0.000) for 2177 atoms. Found 0 (9 requested) and removed 5 (9 requested) atoms. Cycle 47: After refmac, R = 0.1902 (Rfree = 0.000) for 2167 atoms. Found 0 (9 requested) and removed 6 (9 requested) atoms. Cycle 48: After refmac, R = 0.1824 (Rfree = 0.000) for 2160 atoms. Found 0 (9 requested) and removed 4 (9 requested) atoms. Cycle 49: After refmac, R = 0.1775 (Rfree = 0.000) for 2153 atoms. Found 0 (9 requested) and removed 1 (9 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 46.93