Sun 23 Dec 22:22:46 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 1vjn-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-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/1vjn-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-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 22:22:56 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/1vjn-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-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 366 and 0 Target number of residues in the AU: 366 Target solvent content: 0.5397 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-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: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 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 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: 60.370 3.401 Wilson plot Bfac: 32.62 5620 reflections ( 98.11 % complete ) and 0 restraints for refining 3882 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2829 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2464 (Rfree = 0.000) for 3882 atoms. Found 29 (29 requested) and removed 36 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.82 3.01 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 0 residues added, 3908 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 8 peptides. Score 0.336 Round 2: 215 peptides, 36 chains. Longest chain 15 peptides. Score 0.449 Round 3: 249 peptides, 37 chains. Longest chain 13 peptides. Score 0.545 Round 4: 262 peptides, 32 chains. Longest chain 21 peptides. Score 0.642 Round 5: 265 peptides, 38 chains. Longest chain 15 peptides. Score 0.579 Taking the results from Round 4 Chains 32, Residues 230, Estimated correctness of the model 41.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7014 restraints for refining 3194 atoms. 6126 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2258 (Rfree = 0.000) for 3194 atoms. Found 15 (24 requested) and removed 27 (12 requested) atoms. Cycle 2: After refmac, R = 0.2206 (Rfree = 0.000) for 3127 atoms. Found 17 (24 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 3098 atoms. Found 18 (23 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 3074 atoms. Found 11 (23 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.1930 (Rfree = 0.000) for 3060 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.77 2.96 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 3130 seeds are put forward Round 1: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.437 Round 2: 262 peptides, 35 chains. Longest chain 20 peptides. Score 0.607 Round 3: 271 peptides, 33 chains. Longest chain 22 peptides. Score 0.653 Round 4: 273 peptides, 35 chains. Longest chain 22 peptides. Score 0.636 Round 5: 278 peptides, 36 chains. Longest chain 22 peptides. Score 0.637 Taking the results from Round 3 Chains 33, Residues 238, Estimated correctness of the model 45.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6641 restraints for refining 3038 atoms. 5722 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2121 (Rfree = 0.000) for 3038 atoms. Found 15 (22 requested) and removed 22 (11 requested) atoms. Cycle 7: After refmac, R = 0.1920 (Rfree = 0.000) for 3017 atoms. Found 9 (22 requested) and removed 18 (11 requested) atoms. Cycle 8: After refmac, R = 0.1891 (Rfree = 0.000) for 2999 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.1865 (Rfree = 0.000) for 2989 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.1815 (Rfree = 0.000) for 2974 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.80 2.99 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3070 seeds are put forward Round 1: 242 peptides, 37 chains. Longest chain 17 peptides. Score 0.524 Round 2: 246 peptides, 28 chains. Longest chain 24 peptides. Score 0.647 Round 3: 247 peptides, 30 chains. Longest chain 25 peptides. Score 0.627 Round 4: 262 peptides, 29 chains. Longest chain 18 peptides. Score 0.675 Round 5: 264 peptides, 38 chains. Longest chain 18 peptides. Score 0.576 Taking the results from Round 4 Chains 31, Residues 233, Estimated correctness of the model 51.2 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6435 restraints for refining 3097 atoms. 5365 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2070 (Rfree = 0.000) for 3097 atoms. Found 12 (23 requested) and removed 23 (11 requested) atoms. Cycle 12: After refmac, R = 0.1918 (Rfree = 0.000) for 3072 atoms. Found 4 (23 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.1841 (Rfree = 0.000) for 3055 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.1810 (Rfree = 0.000) for 3046 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.1803 (Rfree = 0.000) for 3035 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.74 2.93 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3135 seeds are put forward Round 1: 240 peptides, 41 chains. Longest chain 12 peptides. Score 0.461 Round 2: 260 peptides, 37 chains. Longest chain 18 peptides. Score 0.577 Round 3: 236 peptides, 30 chains. Longest chain 16 peptides. Score 0.597 Round 4: 237 peptides, 33 chains. Longest chain 15 peptides. Score 0.561 Round 5: 252 peptides, 31 chains. Longest chain 19 peptides. Score 0.628 Taking the results from Round 5 Chains 33, Residues 221, Estimated correctness of the model 37.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6929 restraints for refining 3148 atoms. 6004 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2135 (Rfree = 0.000) for 3148 atoms. Found 17 (23 requested) and removed 24 (11 requested) atoms. Cycle 17: After refmac, R = 0.1967 (Rfree = 0.000) for 3131 atoms. Found 13 (23 requested) and removed 17 (11 requested) atoms. Cycle 18: After refmac, R = 0.1921 (Rfree = 0.000) for 3123 atoms. Found 14 (23 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1897 (Rfree = 0.000) for 3125 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.1869 (Rfree = 0.000) for 3114 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.71 2.90 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3199 seeds are put forward Round 1: 206 peptides, 37 chains. Longest chain 13 peptides. Score 0.402 Round 2: 241 peptides, 35 chains. Longest chain 15 peptides. Score 0.547 Round 3: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.559 Round 4: 259 peptides, 38 chains. Longest chain 15 peptides. Score 0.562 Round 5: 253 peptides, 34 chains. Longest chain 16 peptides. Score 0.595 Taking the results from Round 5 Chains 34, Residues 219, Estimated correctness of the model 27.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7098 restraints for refining 3201 atoms. 6228 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2160 (Rfree = 0.000) for 3201 atoms. Found 17 (24 requested) and removed 21 (12 requested) atoms. Cycle 22: After refmac, R = 0.2036 (Rfree = 0.000) for 3185 atoms. Found 12 (24 requested) and removed 18 (12 requested) atoms. Cycle 23: After refmac, R = 0.1912 (Rfree = 0.000) for 3173 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.1886 (Rfree = 0.000) for 3162 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1885 (Rfree = 0.000) for 3154 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.70 2.89 Search for helices and strands: 0 residues in 0 chains, 3208 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3231 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 13 peptides. Score 0.391 Round 2: 219 peptides, 33 chains. Longest chain 18 peptides. Score 0.506 Round 3: 212 peptides, 33 chains. Longest chain 15 peptides. Score 0.483 Round 4: 228 peptides, 32 chains. Longest chain 12 peptides. Score 0.548 Round 5: 236 peptides, 36 chains. Longest chain 12 peptides. Score 0.518 Taking the results from Round 4 Chains 32, Residues 196, Estimated correctness of the model 10.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7254 restraints for refining 3201 atoms. 6459 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2039 (Rfree = 0.000) for 3201 atoms. Found 22 (24 requested) and removed 30 (12 requested) atoms. Cycle 27: After refmac, R = 0.1839 (Rfree = 0.000) for 3180 atoms. Found 9 (24 requested) and removed 19 (12 requested) atoms. Cycle 28: After refmac, R = 0.1825 (Rfree = 0.000) for 3163 atoms. Found 8 (23 requested) and removed 19 (11 requested) atoms. Cycle 29: After refmac, R = 0.1753 (Rfree = 0.000) for 3150 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1697 (Rfree = 0.000) for 3142 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.72 2.91 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3215 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 9 peptides. Score 0.373 Round 2: 208 peptides, 34 chains. Longest chain 14 peptides. Score 0.455 Round 3: 204 peptides, 32 chains. Longest chain 12 peptides. Score 0.471 Round 4: 211 peptides, 32 chains. Longest chain 15 peptides. Score 0.494 Round 5: 193 peptides, 34 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 4 Chains 32, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7338 restraints for refining 3153 atoms. 6654 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2027 (Rfree = 0.000) for 3153 atoms. Found 21 (23 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.1968 (Rfree = 0.000) for 3149 atoms. Found 19 (23 requested) and removed 19 (11 requested) atoms. Cycle 33: After refmac, R = 0.1927 (Rfree = 0.000) for 3141 atoms. Found 21 (23 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1593 (Rfree = 0.000) for 3141 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1578 (Rfree = 0.000) for 3136 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.71 2.90 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3221 seeds are put forward Round 1: 173 peptides, 34 chains. Longest chain 10 peptides. Score 0.324 Round 2: 198 peptides, 35 chains. Longest chain 15 peptides. Score 0.404 Round 3: 210 peptides, 34 chains. Longest chain 17 peptides. Score 0.461 Round 4: 208 peptides, 33 chains. Longest chain 18 peptides. Score 0.469 Round 5: 189 peptides, 29 chains. Longest chain 22 peptides. Score 0.464 Taking the results from Round 4 Chains 33, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7293 restraints for refining 3152 atoms. 6626 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1806 (Rfree = 0.000) for 3152 atoms. Found 22 (23 requested) and removed 19 (11 requested) atoms. Cycle 37: After refmac, R = 0.1651 (Rfree = 0.000) for 3150 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1636 (Rfree = 0.000) for 3136 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 3131 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1611 (Rfree = 0.000) for 3123 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.68 2.87 Search for helices and strands: 0 residues in 0 chains, 3179 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3210 seeds are put forward Round 1: 175 peptides, 32 chains. Longest chain 12 peptides. Score 0.365 Round 2: 188 peptides, 33 chains. Longest chain 15 peptides. Score 0.398 Round 3: 182 peptides, 31 chains. Longest chain 17 peptides. Score 0.408 Round 4: 173 peptides, 32 chains. Longest chain 10 peptides. Score 0.358 Round 5: 190 peptides, 31 chains. Longest chain 19 peptides. Score 0.437 Taking the results from Round 5 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7485 restraints for refining 3186 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1798 (Rfree = 0.000) for 3186 atoms. Found 15 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.1675 (Rfree = 0.000) for 3181 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1638 (Rfree = 0.000) for 3174 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1654 (Rfree = 0.000) for 3163 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1608 (Rfree = 0.000) for 3158 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.68 2.87 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3237 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 7 peptides. Score 0.317 Round 2: 187 peptides, 34 chains. Longest chain 10 peptides. Score 0.379 Round 3: 201 peptides, 33 chains. Longest chain 16 peptides. Score 0.445 Round 4: 198 peptides, 35 chains. Longest chain 13 peptides. Score 0.404 Round 5: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5620 reflections ( 98.11 % complete ) and 7360 restraints for refining 3162 atoms. 6721 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1865 (Rfree = 0.000) for 3162 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1928 (Rfree = 0.000) for 3146 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1689 (Rfree = 0.000) for 3134 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1654 (Rfree = 0.000) for 3122 atoms. TimeTaking 53.58