Mon 24 Dec 00:41:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-mrncs ############### 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 00:42:03 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 3908 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2825 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2374 (Rfree = 0.000) for 3908 atoms. Found 29 (29 requested) and removed 43 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 3.00 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 0 residues added, 3925 seeds are put forward Round 1: 179 peptides, 36 chains. Longest chain 9 peptides. Score 0.315 Round 2: 238 peptides, 38 chains. Longest chain 16 peptides. Score 0.497 Round 3: 250 peptides, 33 chains. Longest chain 23 peptides. Score 0.599 Round 4: 265 peptides, 34 chains. Longest chain 21 peptides. Score 0.627 Round 5: 262 peptides, 33 chains. Longest chain 18 peptides. Score 0.630 Taking the results from Round 5 Chains 33, Residues 229, Estimated correctness of the model 38.1 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6990 restraints for refining 3201 atoms. 6037 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2124 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 19 (12 requested) atoms. Cycle 2: After refmac, R = 0.1989 (Rfree = 0.000) for 3143 atoms. Found 13 (24 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2043 (Rfree = 0.000) for 3110 atoms. Found 15 (23 requested) and removed 17 (11 requested) atoms. Cycle 4: After refmac, R = 0.1913 (Rfree = 0.000) for 3094 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 5: After refmac, R = 0.1854 (Rfree = 0.000) for 3070 atoms. Found 8 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.77 2.96 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 3143 seeds are put forward Round 1: 225 peptides, 36 chains. Longest chain 15 peptides. Score 0.483 Round 2: 257 peptides, 38 chains. Longest chain 18 peptides. Score 0.556 Round 3: 255 peptides, 32 chains. Longest chain 20 peptides. Score 0.624 Round 4: 262 peptides, 34 chains. Longest chain 16 peptides. Score 0.619 Round 5: 251 peptides, 31 chains. Longest chain 20 peptides. Score 0.625 Taking the results from Round 5 Chains 33, Residues 220, Estimated correctness of the model 36.6 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6804 restraints for refining 3108 atoms. 5884 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2147 (Rfree = 0.000) for 3108 atoms. Found 14 (23 requested) and removed 21 (11 requested) atoms. Cycle 7: After refmac, R = 0.2039 (Rfree = 0.000) for 3081 atoms. Found 12 (23 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.2010 (Rfree = 0.000) for 3070 atoms. Found 9 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.1963 (Rfree = 0.000) for 3056 atoms. Found 10 (23 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.1831 (Rfree = 0.000) for 3048 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.78 2.97 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3153 seeds are put forward Round 1: 230 peptides, 39 chains. Longest chain 21 peptides. Score 0.456 Round 2: 262 peptides, 37 chains. Longest chain 13 peptides. Score 0.583 Round 3: 267 peptides, 35 chains. Longest chain 25 peptides. Score 0.620 Round 4: 275 peptides, 36 chains. Longest chain 25 peptides. Score 0.629 Round 5: 279 peptides, 34 chains. Longest chain 25 peptides. Score 0.661 Taking the results from Round 5 Chains 35, Residues 245, Estimated correctness of the model 47.3 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6878 restraints for refining 3174 atoms. 5891 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2166 (Rfree = 0.000) for 3174 atoms. Found 20 (23 requested) and removed 31 (11 requested) atoms. Cycle 12: After refmac, R = 0.1935 (Rfree = 0.000) for 3148 atoms. Found 12 (23 requested) and removed 21 (11 requested) atoms. Cycle 13: After refmac, R = 0.1809 (Rfree = 0.000) for 3129 atoms. Found 3 (23 requested) and removed 19 (11 requested) atoms. Cycle 14: After refmac, R = 0.1736 (Rfree = 0.000) for 3107 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.1707 (Rfree = 0.000) for 3096 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.81 3.00 Search for helices and strands: 0 residues in 0 chains, 3171 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 3208 seeds are put forward Round 1: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.467 Round 2: 250 peptides, 36 chains. Longest chain 14 peptides. Score 0.561 Round 3: 259 peptides, 37 chains. Longest chain 14 peptides. Score 0.574 Round 4: 268 peptides, 36 chains. Longest chain 20 peptides. Score 0.611 Round 5: 257 peptides, 35 chains. Longest chain 18 peptides. Score 0.593 Taking the results from Round 4 Chains 37, Residues 232, Estimated correctness of the model 32.2 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 6874 restraints for refining 3190 atoms. 5862 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2067 (Rfree = 0.000) for 3190 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 17: After refmac, R = 0.1896 (Rfree = 0.000) for 3179 atoms. Found 12 (24 requested) and removed 21 (12 requested) atoms. Cycle 18: After refmac, R = 0.1960 (Rfree = 0.000) for 3159 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1866 (Rfree = 0.000) for 3148 atoms. Found 7 (23 requested) and removed 23 (11 requested) atoms. Cycle 20: After refmac, R = 0.1809 (Rfree = 0.000) for 3129 atoms. Found 10 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.82 3.01 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 3210 seeds are put forward Round 1: 204 peptides, 36 chains. Longest chain 13 peptides. Score 0.410 Round 2: 223 peptides, 36 chains. Longest chain 14 peptides. Score 0.476 Round 3: 237 peptides, 36 chains. Longest chain 16 peptides. Score 0.522 Round 4: 229 peptides, 36 chains. Longest chain 14 peptides. Score 0.496 Round 5: 226 peptides, 33 chains. Longest chain 13 peptides. Score 0.528 Taking the results from Round 5 Chains 33, Residues 193, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7386 restraints for refining 3201 atoms. 6647 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2048 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 17 (12 requested) atoms. Cycle 22: After refmac, R = 0.2028 (Rfree = 0.000) for 3191 atoms. Found 19 (24 requested) and removed 22 (12 requested) atoms. Cycle 23: After refmac, R = 0.1867 (Rfree = 0.000) for 3178 atoms. Found 15 (24 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.1787 (Rfree = 0.000) for 3171 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1707 (Rfree = 0.000) for 3162 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.75 2.94 Search for helices and strands: 0 residues in 0 chains, 3247 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3259 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 11 peptides. Score 0.327 Round 2: 215 peptides, 33 chains. Longest chain 14 peptides. Score 0.493 Round 3: 227 peptides, 34 chains. Longest chain 21 peptides. Score 0.517 Round 4: 208 peptides, 33 chains. Longest chain 14 peptides. Score 0.469 Round 5: 225 peptides, 34 chains. Longest chain 14 peptides. Score 0.511 Taking the results from Round 3 Chains 36, Residues 193, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7000 restraints for refining 3201 atoms. 6109 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1985 (Rfree = 0.000) for 3201 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.1844 (Rfree = 0.000) for 3200 atoms. Found 20 (24 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.1783 (Rfree = 0.000) for 3202 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 29: After refmac, R = 0.1723 (Rfree = 0.000) for 3195 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.1714 (Rfree = 0.000) for 3183 atoms. Found 8 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.72 2.91 Search for helices and strands: 0 residues in 0 chains, 3227 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3243 seeds are put forward Round 1: 173 peptides, 30 chains. Longest chain 15 peptides. Score 0.390 Round 2: 205 peptides, 32 chains. Longest chain 14 peptides. Score 0.474 Round 3: 218 peptides, 32 chains. Longest chain 23 peptides. Score 0.517 Round 4: 216 peptides, 31 chains. Longest chain 23 peptides. Score 0.524 Round 5: 222 peptides, 32 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 5 Chains 32, Residues 190, Estimated correctness of the model 3.7 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5620 reflections ( 98.11 % complete ) and 6980 restraints for refining 3200 atoms. 6140 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1874 (Rfree = 0.000) for 3200 atoms. Found 9 (24 requested) and removed 18 (12 requested) atoms. Cycle 32: After refmac, R = 0.1756 (Rfree = 0.000) for 3185 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.1722 (Rfree = 0.000) for 3171 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 3163 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1707 (Rfree = 0.000) for 3153 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.73 2.92 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 185 peptides, 36 chains. Longest chain 11 peptides. Score 0.338 Round 2: 226 peptides, 39 chains. Longest chain 14 peptides. Score 0.443 Round 3: 218 peptides, 36 chains. Longest chain 15 peptides. Score 0.459 Round 4: 212 peptides, 34 chains. Longest chain 15 peptides. Score 0.468 Round 5: 205 peptides, 31 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 5 Chains 33, Residues 174, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7090 restraints for refining 3201 atoms. 6313 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1882 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.1729 (Rfree = 0.000) for 3189 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.1699 (Rfree = 0.000) for 3178 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1673 (Rfree = 0.000) for 3166 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1673 (Rfree = 0.000) for 3157 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.77 2.96 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3239 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 11 peptides. Score 0.315 Round 2: 184 peptides, 29 chains. Longest chain 16 peptides. Score 0.447 Round 3: 189 peptides, 30 chains. Longest chain 12 peptides. Score 0.449 Round 4: 180 peptides, 25 chains. Longest chain 14 peptides. Score 0.494 Round 5: 186 peptides, 28 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 4 Chains 25, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5620 reflections ( 98.11 % complete ) and 7394 restraints for refining 3201 atoms. 6799 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1851 (Rfree = 0.000) for 3201 atoms. Found 10 (24 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.1697 (Rfree = 0.000) for 3194 atoms. Found 4 (24 requested) and removed 17 (12 requested) atoms. Cycle 43: After refmac, R = 0.1706 (Rfree = 0.000) for 3179 atoms. Found 7 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1703 (Rfree = 0.000) for 3174 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1679 (Rfree = 0.000) for 3168 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.75 2.94 Search for helices and strands: 0 residues in 0 chains, 3223 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3246 seeds are put forward Round 1: 171 peptides, 31 chains. Longest chain 12 peptides. Score 0.366 Round 2: 173 peptides, 30 chains. Longest chain 14 peptides. Score 0.390 Round 3: 180 peptides, 29 chains. Longest chain 13 peptides. Score 0.432 Round 4: 185 peptides, 30 chains. Longest chain 16 peptides. Score 0.435 Round 5: 183 peptides, 29 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 154, 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 7480 restraints for refining 3194 atoms. 6893 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1811 (Rfree = 0.000) for 3194 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1788 (Rfree = 0.000) for 3180 atoms. Found 0 (24 requested) and removed 6 (12 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1623 (Rfree = 0.000) for 3171 atoms. Found 0 (23 requested) and removed 3 (11 requested) atoms. Cycle 49: After refmac, R = 0.1612 (Rfree = 0.000) for 3166 atoms. TimeTaking 43.17