null Sun 23 Dec 22:22:40 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 1vk4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.4-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/1vk4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.4-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 22:22:49 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/1vk4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.4-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 207 and 0 Target number of residues in the AU: 207 Target solvent content: 0.6071 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: 1vk4-3.4-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: 1vk4-3.4-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 3.400 Wilson plot Bfac: 55.00 4213 reflections ( 99.25 % complete ) and 0 restraints for refining 2642 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2957 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2605 (Rfree = 0.000) for 2642 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 2690 seeds are put forward Round 1: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.372 Round 2: 168 peptides, 25 chains. Longest chain 13 peptides. Score 0.549 Round 3: 181 peptides, 27 chains. Longest chain 16 peptides. Score 0.568 Round 4: 198 peptides, 25 chains. Longest chain 18 peptides. Score 0.668 Round 5: 196 peptides, 24 chains. Longest chain 20 peptides. Score 0.677 Taking the results from Round 5 Chains 24, Residues 172, Estimated correctness of the model 51.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4461 restraints for refining 2168 atoms. 3767 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 2168 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2438 (Rfree = 0.000) for 2130 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 2123 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2220 (Rfree = 0.000) for 2114 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 5: After refmac, R = 0.2184 (Rfree = 0.000) for 2105 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 2181 seeds are put forward Round 1: 162 peptides, 25 chains. Longest chain 13 peptides. Score 0.521 Round 2: 184 peptides, 24 chains. Longest chain 14 peptides. Score 0.634 Round 3: 186 peptides, 25 chains. Longest chain 24 peptides. Score 0.624 Round 4: 181 peptides, 24 chains. Longest chain 19 peptides. Score 0.622 Round 5: 185 peptides, 24 chains. Longest chain 35 peptides. Score 0.638 Taking the results from Round 5 Chains 24, Residues 161, Estimated correctness of the model 40.6 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4374 restraints for refining 2168 atoms. 3590 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2547 (Rfree = 0.000) for 2168 atoms. Found 13 (16 requested) and removed 20 (8 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 2148 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 2140 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2264 (Rfree = 0.000) for 2129 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2214 (Rfree = 0.000) for 2119 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.41 Search for helices and strands: 0 residues in 0 chains, 2179 seeds are put forward Round 1: 174 peptides, 27 chains. Longest chain 17 peptides. Score 0.537 Round 2: 192 peptides, 25 chains. Longest chain 20 peptides. Score 0.647 Round 3: 202 peptides, 24 chains. Longest chain 19 peptides. Score 0.697 Round 4: 190 peptides, 21 chains. Longest chain 30 peptides. Score 0.702 Round 5: 196 peptides, 25 chains. Longest chain 15 peptides. Score 0.661 Taking the results from Round 4 Chains 21, Residues 169, Estimated correctness of the model 58.4 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4412 restraints for refining 2168 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2583 (Rfree = 0.000) for 2168 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. Cycle 12: After refmac, R = 0.2313 (Rfree = 0.000) for 2162 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.2192 (Rfree = 0.000) for 2152 atoms. Found 1 (15 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2135 (Rfree = 0.000) for 2138 atoms. Found 4 (15 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2088 (Rfree = 0.000) for 2129 atoms. Found 5 (15 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.37 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward Round 1: 173 peptides, 26 chains. Longest chain 22 peptides. Score 0.552 Round 2: 180 peptides, 22 chains. Longest chain 18 peptides. Score 0.652 Round 3: 176 peptides, 23 chains. Longest chain 16 peptides. Score 0.620 Round 4: 178 peptides, 21 chains. Longest chain 21 peptides. Score 0.662 Round 5: 173 peptides, 20 chains. Longest chain 18 peptides. Score 0.660 Taking the results from Round 4 Chains 21, Residues 157, Estimated correctness of the model 47.6 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4821 restraints for refining 2168 atoms. 4188 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2184 (Rfree = 0.000) for 2168 atoms. Found 9 (14 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2160 (Rfree = 0.000) for 2161 atoms. Found 9 (14 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.1898 (Rfree = 0.000) for 2157 atoms. Found 4 (14 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1856 (Rfree = 0.000) for 2148 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1748 (Rfree = 0.000) for 2140 atoms. Found 3 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 2187 seeds are put forward Round 1: 158 peptides, 21 chains. Longest chain 17 peptides. Score 0.583 Round 2: 179 peptides, 20 chains. Longest chain 18 peptides. Score 0.681 Round 3: 181 peptides, 24 chains. Longest chain 18 peptides. Score 0.622 Round 4: 180 peptides, 21 chains. Longest chain 19 peptides. Score 0.669 Round 5: 170 peptides, 19 chains. Longest chain 18 peptides. Score 0.666 Taking the results from Round 2 Chains 21, Residues 159, Estimated correctness of the model 52.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4693 restraints for refining 2168 atoms. 4028 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1910 (Rfree = 0.000) for 2168 atoms. Found 7 (14 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.1801 (Rfree = 0.000) for 2160 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 2156 atoms. Found 4 (14 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1783 (Rfree = 0.000) for 2150 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1766 (Rfree = 0.000) for 2142 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.36 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward Round 1: 163 peptides, 24 chains. Longest chain 17 peptides. Score 0.546 Round 2: 168 peptides, 20 chains. Longest chain 20 peptides. Score 0.641 Round 3: 176 peptides, 21 chains. Longest chain 19 peptides. Score 0.654 Round 4: 174 peptides, 19 chains. Longest chain 19 peptides. Score 0.680 Round 5: 177 peptides, 22 chains. Longest chain 19 peptides. Score 0.641 Taking the results from Round 4 Chains 19, Residues 155, Estimated correctness of the model 52.6 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4694 restraints for refining 2168 atoms. 4052 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2077 (Rfree = 0.000) for 2168 atoms. Found 7 (14 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.1966 (Rfree = 0.000) for 2157 atoms. Found 3 (14 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.1919 (Rfree = 0.000) for 2149 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1846 (Rfree = 0.000) for 2140 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1805 (Rfree = 0.000) for 2138 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 2210 seeds are put forward Round 1: 148 peptides, 21 chains. Longest chain 14 peptides. Score 0.538 Round 2: 171 peptides, 22 chains. Longest chain 18 peptides. Score 0.618 Round 3: 155 peptides, 20 chains. Longest chain 19 peptides. Score 0.589 Round 4: 156 peptides, 22 chains. Longest chain 15 peptides. Score 0.554 Round 5: 170 peptides, 23 chains. Longest chain 15 peptides. Score 0.596 Taking the results from Round 2 Chains 22, Residues 149, Estimated correctness of the model 34.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4918 restraints for refining 2163 atoms. 4344 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1878 (Rfree = 0.000) for 2163 atoms. Found 10 (14 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.1781 (Rfree = 0.000) for 2163 atoms. Found 5 (14 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1760 (Rfree = 0.000) for 2157 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1740 (Rfree = 0.000) for 2151 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1719 (Rfree = 0.000) for 2146 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward Round 1: 139 peptides, 22 chains. Longest chain 15 peptides. Score 0.472 Round 2: 163 peptides, 24 chains. Longest chain 15 peptides. Score 0.546 Round 3: 159 peptides, 22 chains. Longest chain 16 peptides. Score 0.568 Round 4: 156 peptides, 20 chains. Longest chain 17 peptides. Score 0.593 Round 5: 158 peptides, 22 chains. Longest chain 15 peptides. Score 0.563 Taking the results from Round 4 Chains 20, Residues 136, Estimated correctness of the model 26.4 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4878 restraints for refining 2168 atoms. 4314 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2089 (Rfree = 0.000) for 2168 atoms. Found 14 (14 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.1924 (Rfree = 0.000) for 2169 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1904 (Rfree = 0.000) for 2165 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 2157 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1840 (Rfree = 0.000) for 2152 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward Round 1: 127 peptides, 23 chains. Longest chain 12 peptides. Score 0.385 Round 2: 160 peptides, 23 chains. Longest chain 13 peptides. Score 0.552 Round 3: 151 peptides, 22 chains. Longest chain 15 peptides. Score 0.531 Round 4: 163 peptides, 24 chains. Longest chain 19 peptides. Score 0.546 Round 5: 166 peptides, 23 chains. Longest chain 20 peptides. Score 0.579 Taking the results from Round 5 Chains 23, Residues 143, Estimated correctness of the model 21.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4213 reflections ( 99.25 % complete ) and 4934 restraints for refining 2168 atoms. 4385 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 2168 atoms. Found 12 (14 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1888 (Rfree = 0.000) for 2171 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1827 (Rfree = 0.000) for 2166 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1805 (Rfree = 0.000) for 2158 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1856 (Rfree = 0.000) for 2153 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 2211 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.412 Round 2: 138 peptides, 20 chains. Longest chain 14 peptides. Score 0.511 Round 3: 142 peptides, 20 chains. Longest chain 16 peptides. Score 0.530 Round 4: 143 peptides, 19 chains. Longest chain 18 peptides. Score 0.556 Round 5: 145 peptides, 19 chains. Longest chain 15 peptides. Score 0.565 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 126, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vk4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4213 reflections ( 99.25 % complete ) and 4967 restraints for refining 2168 atoms. 4482 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2081 (Rfree = 0.000) for 2168 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1864 (Rfree = 0.000) for 2158 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2079 (Rfree = 0.000) for 2149 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1671 (Rfree = 0.000) for 2140 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:06 GMT 2018 Job finished. TimeTaking 43.42 Used memory is bytes: 7336664