Sun 23 Dec 22:23:14 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-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 22:23:22 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.5649 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 39.98 4736 reflections ( 98.07 % complete ) and 0 restraints for refining 3883 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.2822 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1949 (Rfree = 0.000) for 3883 atoms. Found 12 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.25 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: 141 peptides, 29 chains. Longest chain 8 peptides. Score 0.279 Round 2: 183 peptides, 33 chains. Longest chain 9 peptides. Score 0.380 Round 3: 216 peptides, 33 chains. Longest chain 13 peptides. Score 0.496 Round 4: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.495 Round 5: 232 peptides, 35 chains. Longest chain 13 peptides. Score 0.519 Taking the results from Round 5 Chains 35, Residues 197, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7377 restraints for refining 3190 atoms. 6581 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2082 (Rfree = 0.000) for 3190 atoms. Found 15 (20 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.1972 (Rfree = 0.000) for 3137 atoms. Found 11 (20 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.1903 (Rfree = 0.000) for 3109 atoms. Found 9 (20 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.1787 (Rfree = 0.000) for 3090 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.1780 (Rfree = 0.000) for 3066 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 3142 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3157 seeds are put forward Round 1: 179 peptides, 33 chains. Longest chain 12 peptides. Score 0.364 Round 2: 228 peptides, 33 chains. Longest chain 14 peptides. Score 0.534 Round 3: 244 peptides, 38 chains. Longest chain 15 peptides. Score 0.516 Round 4: 220 peptides, 29 chains. Longest chain 14 peptides. Score 0.564 Round 5: 225 peptides, 31 chains. Longest chain 17 peptides. Score 0.552 Taking the results from Round 4 Chains 29, Residues 191, Estimated correctness of the model 0.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 6940 restraints for refining 3045 atoms. 6205 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2070 (Rfree = 0.000) for 3045 atoms. Found 14 (19 requested) and removed 24 (9 requested) atoms. Cycle 7: After refmac, R = 0.2032 (Rfree = 0.000) for 3027 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2074 (Rfree = 0.000) for 3009 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.2134 (Rfree = 0.000) for 3002 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.1662 (Rfree = 0.000) for 2994 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 0 residues added, 3060 seeds are put forward Round 1: 201 peptides, 38 chains. Longest chain 11 peptides. Score 0.367 Round 2: 222 peptides, 35 chains. Longest chain 13 peptides. Score 0.487 Round 3: 234 peptides, 37 chains. Longest chain 11 peptides. Score 0.498 Round 4: 217 peptides, 33 chains. Longest chain 12 peptides. Score 0.499 Round 5: 238 peptides, 32 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 5 Chains 34, Residues 206, Estimated correctness of the model 5.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 6851 restraints for refining 3059 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2079 (Rfree = 0.000) for 3059 atoms. Found 16 (19 requested) and removed 29 (9 requested) atoms. Cycle 12: After refmac, R = 0.2118 (Rfree = 0.000) for 3024 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 13: After refmac, R = 0.1699 (Rfree = 0.000) for 3004 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.1617 (Rfree = 0.000) for 2998 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.1591 (Rfree = 0.000) for 2988 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3080 seeds are put forward Round 1: 188 peptides, 35 chains. Longest chain 12 peptides. Score 0.366 Round 2: 219 peptides, 35 chains. Longest chain 14 peptides. Score 0.477 Round 3: 216 peptides, 31 chains. Longest chain 14 peptides. Score 0.524 Round 4: 238 peptides, 38 chains. Longest chain 15 peptides. Score 0.497 Round 5: 227 peptides, 34 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 3 Chains 31, Residues 185, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 6888 restraints for refining 3026 atoms. 6140 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1967 (Rfree = 0.000) for 3026 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 17: After refmac, R = 0.1872 (Rfree = 0.000) for 3004 atoms. Found 18 (19 requested) and removed 19 (9 requested) atoms. Cycle 18: After refmac, R = 0.1786 (Rfree = 0.000) for 2996 atoms. Found 13 (19 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.1822 (Rfree = 0.000) for 2995 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.1906 (Rfree = 0.000) for 2990 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 3065 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3079 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 12 peptides. Score 0.373 Round 2: 207 peptides, 32 chains. Longest chain 12 peptides. Score 0.481 Round 3: 217 peptides, 34 chains. Longest chain 17 peptides. Score 0.485 Round 4: 213 peptides, 35 chains. Longest chain 12 peptides. Score 0.457 Round 5: 217 peptides, 34 chains. Longest chain 14 peptides. Score 0.485 Taking the results from Round 5 Chains 35, Residues 183, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7054 restraints for refining 3089 atoms. 6320 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1818 (Rfree = 0.000) for 3089 atoms. Found 12 (19 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.1651 (Rfree = 0.000) for 3070 atoms. Found 10 (19 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.1494 (Rfree = 0.000) for 3060 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.1515 (Rfree = 0.000) for 3054 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1592 (Rfree = 0.000) for 3044 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 3136 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3155 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 9 peptides. Score 0.350 Round 2: 217 peptides, 37 chains. Longest chain 11 peptides. Score 0.441 Round 3: 202 peptides, 33 chains. Longest chain 11 peptides. Score 0.449 Round 4: 200 peptides, 30 chains. Longest chain 20 peptides. Score 0.487 Round 5: 211 peptides, 34 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 4 Chains 31, Residues 170, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7132 restraints for refining 3137 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1745 (Rfree = 0.000) for 3137 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 27: After refmac, R = 0.1639 (Rfree = 0.000) for 3117 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 28: After refmac, R = 0.1556 (Rfree = 0.000) for 3109 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.1505 (Rfree = 0.000) for 3103 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1471 (Rfree = 0.000) for 3095 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3186 seeds are put forward Round 1: 175 peptides, 33 chains. Longest chain 13 peptides. Score 0.349 Round 2: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.450 Round 3: 213 peptides, 32 chains. Longest chain 24 peptides. Score 0.501 Round 4: 210 peptides, 30 chains. Longest chain 17 peptides. Score 0.519 Round 5: 212 peptides, 34 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 30, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7429 restraints for refining 3189 atoms. 6739 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1796 (Rfree = 0.000) for 3189 atoms. Found 13 (20 requested) and removed 27 (10 requested) atoms. Cycle 32: After refmac, R = 0.1643 (Rfree = 0.000) for 3171 atoms. Found 3 (20 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.1666 (Rfree = 0.000) for 3157 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.1632 (Rfree = 0.000) for 3151 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1630 (Rfree = 0.000) for 3142 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 3.18 Search for helices and strands: 0 residues in 0 chains, 3198 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3213 seeds are put forward Round 1: 196 peptides, 39 chains. Longest chain 11 peptides. Score 0.332 Round 2: 206 peptides, 37 chains. Longest chain 11 peptides. Score 0.402 Round 3: 212 peptides, 35 chains. Longest chain 16 peptides. Score 0.453 Round 4: 195 peptides, 32 chains. Longest chain 12 peptides. Score 0.439 Round 5: 191 peptides, 29 chains. Longest chain 16 peptides. Score 0.471 Taking the results from Round 5 Chains 29, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7607 restraints for refining 3191 atoms. 6988 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1743 (Rfree = 0.000) for 3191 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.1714 (Rfree = 0.000) for 3182 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.1631 (Rfree = 0.000) for 3174 atoms. Found 14 (20 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1766 (Rfree = 0.000) for 3168 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1631 (Rfree = 0.000) for 3168 atoms. Found 15 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 3.18 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3243 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 11 peptides. Score 0.284 Round 2: 181 peptides, 31 chains. Longest chain 15 peptides. Score 0.404 Round 3: 182 peptides, 33 chains. Longest chain 12 peptides. Score 0.376 Round 4: 199 peptides, 33 chains. Longest chain 15 peptides. Score 0.438 Round 5: 185 peptides, 31 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 4 Chains 33, Residues 166, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7459 restraints for refining 3191 atoms. 6792 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1826 (Rfree = 0.000) for 3191 atoms. Found 19 (20 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.1611 (Rfree = 0.000) for 3182 atoms. Found 15 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1696 (Rfree = 0.000) for 3180 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.1676 (Rfree = 0.000) for 3174 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1608 (Rfree = 0.000) for 3173 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 3258 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3276 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 8 peptides. Score 0.267 Round 2: 138 peptides, 26 chains. Longest chain 12 peptides. Score 0.320 Round 3: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.332 Round 4: 155 peptides, 27 chains. Longest chain 11 peptides. Score 0.371 Round 5: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 122, 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. 4736 reflections ( 98.07 % complete ) and 7653 restraints for refining 3190 atoms. 7188 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1629 (Rfree = 0.000) for 3190 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1727 (Rfree = 0.000) for 3175 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1761 (Rfree = 0.000) for 3162 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1483 (Rfree = 0.000) for 3148 atoms. TimeTaking 52.12