null Sun 23 Dec 22:23:01 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 2prv-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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/2prv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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 22:23:10 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/2prv-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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 204 and 0 Target number of residues in the AU: 204 Target solvent content: 0.6415 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.75 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 44.420 3.401 Wilson plot Bfac: 71.97 4000 reflections ( 97.75 % complete ) and 0 restraints for refining 2738 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3781 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3222 (Rfree = 0.000) for 2738 atoms. Found 4 (20 requested) and removed 63 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2699 seeds are put forward NCS extension: 0 residues added, 2699 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 6 peptides. Score 0.187 Round 2: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.242 Round 3: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.257 Round 4: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.315 Round 5: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.278 Taking the results from Round 4 Chains 17, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5233 restraints for refining 2226 atoms. 4954 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2407 (Rfree = 0.000) for 2226 atoms. Found 10 (16 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2482 (Rfree = 0.000) for 2209 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 3: After refmac, R = 0.2428 (Rfree = 0.000) for 2204 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2348 (Rfree = 0.000) for 2194 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 2185 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 0 residues added, 2227 seeds are put forward Round 1: 107 peptides, 25 chains. Longest chain 5 peptides. Score 0.210 Round 2: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.305 Round 3: 130 peptides, 24 chains. Longest chain 9 peptides. Score 0.366 Round 4: 109 peptides, 21 chains. Longest chain 10 peptides. Score 0.320 Round 5: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 3 Chains 24, Residues 106, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5065 restraints for refining 2226 atoms. 4646 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2252 (Rfree = 0.000) for 2226 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. Cycle 7: After refmac, R = 0.2049 (Rfree = 0.000) for 2218 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 2206 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2099 (Rfree = 0.000) for 2204 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.1868 (Rfree = 0.000) for 2196 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.47 Search for helices and strands: 0 residues in 0 chains, 2223 seeds are put forward NCS extension: 0 residues added, 2223 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 8 peptides. Score 0.271 Round 2: 127 peptides, 23 chains. Longest chain 11 peptides. Score 0.373 Round 3: 123 peptides, 20 chains. Longest chain 11 peptides. Score 0.420 Round 4: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.379 Round 5: 133 peptides, 21 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 5 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4958 restraints for refining 2226 atoms. 4504 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2001 (Rfree = 0.000) for 2226 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.1873 (Rfree = 0.000) for 2213 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.1813 (Rfree = 0.000) for 2204 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.1643 (Rfree = 0.000) for 2196 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 2189 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 0 residues added, 2232 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.264 Round 2: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.351 Round 3: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.402 Round 4: 124 peptides, 23 chains. Longest chain 9 peptides. Score 0.356 Round 5: 134 peptides, 22 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4888 restraints for refining 2226 atoms. 4428 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1940 (Rfree = 0.000) for 2226 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. Cycle 17: After refmac, R = 0.1876 (Rfree = 0.000) for 2222 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 2213 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1977 (Rfree = 0.000) for 2205 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1784 (Rfree = 0.000) for 2202 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward NCS extension: 0 residues added, 2235 seeds are put forward Round 1: 125 peptides, 28 chains. Longest chain 7 peptides. Score 0.244 Round 2: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.371 Round 3: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.389 Round 4: 136 peptides, 25 chains. Longest chain 15 peptides. Score 0.375 Round 5: 131 peptides, 25 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 3 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4785 restraints for refining 2226 atoms. 4345 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1861 (Rfree = 0.000) for 2226 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.1857 (Rfree = 0.000) for 2217 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1754 (Rfree = 0.000) for 2215 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1831 (Rfree = 0.000) for 2207 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1783 (Rfree = 0.000) for 2203 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2241 seeds are put forward Round 1: 121 peptides, 26 chains. Longest chain 7 peptides. Score 0.269 Round 2: 129 peptides, 24 chains. Longest chain 12 peptides. Score 0.361 Round 3: 126 peptides, 23 chains. Longest chain 15 peptides. Score 0.367 Round 4: 131 peptides, 24 chains. Longest chain 14 peptides. Score 0.371 Round 5: 126 peptides, 22 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 5 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4891 restraints for refining 2224 atoms. 4497 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1868 (Rfree = 0.000) for 2224 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.2136 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1836 (Rfree = 0.000) for 2229 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.1766 (Rfree = 0.000) for 2227 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1573 (Rfree = 0.000) for 2223 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2255 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2266 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 11 peptides. Score 0.278 Round 2: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.365 Round 3: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.400 Round 4: 127 peptides, 22 chains. Longest chain 13 peptides. Score 0.395 Round 5: 132 peptides, 21 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 5 Chains 22, Residues 111, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4702 restraints for refining 2226 atoms. 4240 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1997 (Rfree = 0.000) for 2226 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.1787 (Rfree = 0.000) for 2215 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1685 (Rfree = 0.000) for 2204 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1692 (Rfree = 0.000) for 2200 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.1671 (Rfree = 0.000) for 2195 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 0 residues added, 2221 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.242 Round 2: 116 peptides, 21 chains. Longest chain 14 peptides. Score 0.359 Round 3: 114 peptides, 21 chains. Longest chain 14 peptides. Score 0.348 Round 4: 99 peptides, 18 chains. Longest chain 14 peptides. Score 0.337 Round 5: 112 peptides, 20 chains. Longest chain 14 peptides. Score 0.361 Taking the results from Round 5 Chains 20, Residues 92, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4977 restraints for refining 2226 atoms. 4616 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1832 (Rfree = 0.000) for 2226 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1779 (Rfree = 0.000) for 2216 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1879 (Rfree = 0.000) for 2212 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1867 (Rfree = 0.000) for 2217 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.1631 (Rfree = 0.000) for 2213 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.49 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 0 residues added, 2247 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.259 Round 2: 99 peptides, 18 chains. Longest chain 14 peptides. Score 0.337 Round 3: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.287 Round 4: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.346 Round 5: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.323 Taking the results from Round 4 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5110 restraints for refining 2226 atoms. 4822 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2842 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.1972 (Rfree = 0.000) for 2208 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1778 (Rfree = 0.000) for 2211 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.1660 (Rfree = 0.000) for 2207 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1555 (Rfree = 0.000) for 2201 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward NCS extension: 0 residues added, 2235 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 7 peptides. Score 0.207 Round 2: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.271 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 4: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.297 Round 5: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.329 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 73, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2prv-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (73 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4000 reflections ( 97.75 % complete ) and 4998 restraints for refining 2196 atoms. 4715 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2567 (Rfree = 0.000) for 2196 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1671 (Rfree = 0.000) for 2176 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1545 (Rfree = 0.000) for 2165 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1495 (Rfree = 0.000) for 2155 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:34 GMT 2018 Job finished. TimeTaking 42.54 Used memory is bytes: 999368