Mon 24 Dec 07:33:12 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:33:17 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/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 3520 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 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 3893 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2850 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2466 (Rfree = 0.000) for 3893 atoms. Found 29 (29 requested) and removed 47 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 3.05 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 0 residues added, 3924 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 7 peptides. Score 0.247 Round 2: 195 peptides, 37 chains. Longest chain 9 peptides. Score 0.361 Round 3: 211 peptides, 37 chains. Longest chain 14 peptides. Score 0.420 Round 4: 222 peptides, 38 chains. Longest chain 10 peptides. Score 0.443 Round 5: 237 peptides, 36 chains. Longest chain 13 peptides. Score 0.522 Taking the results from Round 5 Chains 36, Residues 201, Estimated correctness of the model 1.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7299 restraints for refining 3201 atoms. 6531 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2151 (Rfree = 0.000) for 3201 atoms. Found 13 (24 requested) and removed 23 (12 requested) atoms. Cycle 2: After refmac, R = 0.1969 (Rfree = 0.000) for 3146 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 3: After refmac, R = 0.1886 (Rfree = 0.000) for 3127 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.1872 (Rfree = 0.000) for 3112 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.1849 (Rfree = 0.000) for 3102 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.80 2.99 Search for helices and strands: 0 residues in 0 chains, 3156 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 3168 seeds are put forward Round 1: 213 peptides, 40 chains. Longest chain 10 peptides. Score 0.381 Round 2: 218 peptides, 32 chains. Longest chain 14 peptides. Score 0.517 Round 3: 229 peptides, 34 chains. Longest chain 15 peptides. Score 0.524 Round 4: 249 peptides, 36 chains. Longest chain 14 peptides. Score 0.558 Round 5: 249 peptides, 34 chains. Longest chain 16 peptides. Score 0.583 Taking the results from Round 5 Chains 35, Residues 215, Estimated correctness of the model 23.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6814 restraints for refining 3105 atoms. 5949 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2121 (Rfree = 0.000) for 3105 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 7: After refmac, R = 0.2063 (Rfree = 0.000) for 3092 atoms. Found 17 (23 requested) and removed 19 (11 requested) atoms. Cycle 8: After refmac, R = 0.1916 (Rfree = 0.000) for 3078 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.1795 (Rfree = 0.000) for 3061 atoms. Found 16 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.1775 (Rfree = 0.000) for 3056 atoms. Found 12 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.77 2.96 Search for helices and strands: 0 residues in 0 chains, 3147 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3162 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 10 peptides. Score 0.347 Round 2: 234 peptides, 36 chains. Longest chain 13 peptides. Score 0.512 Round 3: 239 peptides, 34 chains. Longest chain 18 peptides. Score 0.554 Round 4: 249 peptides, 36 chains. Longest chain 16 peptides. Score 0.558 Round 5: 250 peptides, 33 chains. Longest chain 18 peptides. Score 0.599 Taking the results from Round 5 Chains 36, Residues 217, Estimated correctness of the model 28.3 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6541 restraints for refining 3138 atoms. 5605 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2106 (Rfree = 0.000) for 3138 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 12: After refmac, R = 0.2011 (Rfree = 0.000) for 3116 atoms. Found 21 (23 requested) and removed 23 (11 requested) atoms. Cycle 13: After refmac, R = 0.1835 (Rfree = 0.000) for 3101 atoms. Found 14 (23 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.1764 (Rfree = 0.000) for 3084 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.1678 (Rfree = 0.000) for 3073 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.79 2.98 Search for helices and strands: 0 residues in 0 chains, 3136 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3153 seeds are put forward Round 1: 204 peptides, 38 chains. Longest chain 11 peptides. Score 0.379 Round 2: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.467 Round 3: 239 peptides, 38 chains. Longest chain 13 peptides. Score 0.500 Round 4: 240 peptides, 40 chains. Longest chain 14 peptides. Score 0.475 Round 5: 247 peptides, 39 chains. Longest chain 12 peptides. Score 0.512 Taking the results from Round 5 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7200 restraints for refining 3181 atoms. 6407 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2101 (Rfree = 0.000) for 3181 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 17: After refmac, R = 0.2011 (Rfree = 0.000) for 3170 atoms. Found 17 (23 requested) and removed 19 (11 requested) atoms. Cycle 18: After refmac, R = 0.1785 (Rfree = 0.000) for 3163 atoms. Found 13 (23 requested) and removed 21 (11 requested) atoms. Cycle 19: After refmac, R = 0.1797 (Rfree = 0.000) for 3151 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 3145 atoms. Found 15 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.87 3.07 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3215 seeds are put forward Round 1: 191 peptides, 37 chains. Longest chain 11 peptides. Score 0.345 Round 2: 225 peptides, 35 chains. Longest chain 20 peptides. Score 0.497 Round 3: 228 peptides, 36 chains. Longest chain 15 peptides. Score 0.493 Round 4: 222 peptides, 34 chains. Longest chain 15 peptides. Score 0.501 Round 5: 228 peptides, 35 chains. Longest chain 15 peptides. Score 0.507 Taking the results from Round 5 Chains 35, Residues 193, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7296 restraints for refining 3200 atoms. 6512 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2029 (Rfree = 0.000) for 3200 atoms. Found 22 (24 requested) and removed 30 (12 requested) atoms. Cycle 22: After refmac, R = 0.1809 (Rfree = 0.000) for 3187 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.1820 (Rfree = 0.000) for 3173 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1808 (Rfree = 0.000) for 3162 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1774 (Rfree = 0.000) for 3152 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.82 3.01 Search for helices and strands: 0 residues in 0 chains, 3219 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3241 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 13 peptides. Score 0.350 Round 2: 212 peptides, 34 chains. Longest chain 16 peptides. Score 0.468 Round 3: 233 peptides, 39 chains. Longest chain 13 peptides. Score 0.466 Round 4: 235 peptides, 38 chains. Longest chain 11 peptides. Score 0.487 Round 5: 221 peptides, 35 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 38, Residues 197, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7263 restraints for refining 3201 atoms. 6479 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1956 (Rfree = 0.000) for 3201 atoms. Found 10 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.1827 (Rfree = 0.000) for 3185 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.1785 (Rfree = 0.000) for 3171 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1784 (Rfree = 0.000) for 3158 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1794 (Rfree = 0.000) for 3147 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.79 2.98 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 11 peptides. Score 0.374 Round 2: 219 peptides, 33 chains. Longest chain 17 peptides. Score 0.506 Round 3: 221 peptides, 34 chains. Longest chain 17 peptides. Score 0.498 Round 4: 224 peptides, 34 chains. Longest chain 14 peptides. Score 0.508 Round 5: 210 peptides, 32 chains. Longest chain 16 peptides. Score 0.491 Taking the results from Round 4 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7349 restraints for refining 3179 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2140 (Rfree = 0.000) for 3179 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 32: After refmac, R = 0.2050 (Rfree = 0.000) for 3176 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 3179 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.1660 (Rfree = 0.000) for 3177 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.1670 (Rfree = 0.000) for 3167 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.80 2.99 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3238 seeds are put forward Round 1: 171 peptides, 32 chains. Longest chain 14 peptides. Score 0.350 Round 2: 204 peptides, 34 chains. Longest chain 17 peptides. Score 0.441 Round 3: 199 peptides, 35 chains. Longest chain 15 peptides. Score 0.407 Round 4: 205 peptides, 34 chains. Longest chain 16 peptides. Score 0.444 Round 5: 202 peptides, 33 chains. Longest chain 20 peptides. Score 0.449 Taking the results from Round 5 Chains 33, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7470 restraints for refining 3166 atoms. 6827 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1951 (Rfree = 0.000) for 3166 atoms. Found 18 (23 requested) and removed 20 (11 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 3158 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.1737 (Rfree = 0.000) for 3153 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.1625 (Rfree = 0.000) for 3142 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1682 (Rfree = 0.000) for 3132 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.79 2.98 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3253 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 15 peptides. Score 0.380 Round 2: 210 peptides, 36 chains. Longest chain 14 peptides. Score 0.431 Round 3: 202 peptides, 32 chains. Longest chain 20 peptides. Score 0.464 Round 4: 211 peptides, 32 chains. Longest chain 16 peptides. Score 0.494 Round 5: 202 peptides, 33 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 4 Chains 33, Residues 179, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7055 restraints for refining 3164 atoms. 6313 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1883 (Rfree = 0.000) for 3164 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.1710 (Rfree = 0.000) for 3166 atoms. Found 10 (23 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.1662 (Rfree = 0.000) for 3160 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1602 (Rfree = 0.000) for 3156 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1559 (Rfree = 0.000) for 3153 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.76 2.95 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3230 seeds are put forward Round 1: 136 peptides, 25 chains. Longest chain 11 peptides. Score 0.330 Round 2: 166 peptides, 30 chains. Longest chain 11 peptides. Score 0.364 Round 3: 166 peptides, 30 chains. Longest chain 11 peptides. Score 0.364 Round 4: 171 peptides, 28 chains. Longest chain 12 peptides. Score 0.415 Round 5: 169 peptides, 28 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 143, 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 7419 restraints for refining 3153 atoms. 6875 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1766 (Rfree = 0.000) for 3153 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1685 (Rfree = 0.000) for 3139 atoms. Found 0 (23 requested) and removed 8 (11 requested) atoms. Cycle 48: After refmac, R = 0.1671 (Rfree = 0.000) for 3130 atoms. Found 0 (23 requested) and removed 3 (11 requested) atoms. Cycle 49: After refmac, R = 0.1657 (Rfree = 0.000) for 3125 atoms. TimeTaking 40.4