Mon 24 Dec 07:31:26 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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 07:31:31 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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 381 and 0 Target number of residues in the AU: 381 Target solvent content: 0.5209 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 28.02 6759 reflections ( 98.21 % complete ) and 0 restraints for refining 3912 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2858 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2335 (Rfree = 0.000) for 3912 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.66 2.84 Search for helices and strands: 0 residues in 0 chains, 3966 seeds are put forward NCS extension: 0 residues added, 3966 seeds are put forward Round 1: 171 peptides, 35 chains. Longest chain 8 peptides. Score 0.299 Round 2: 220 peptides, 37 chains. Longest chain 12 peptides. Score 0.451 Round 3: 239 peptides, 36 chains. Longest chain 12 peptides. Score 0.528 Round 4: 241 peptides, 31 chains. Longest chain 27 peptides. Score 0.598 Round 5: 246 peptides, 34 chains. Longest chain 20 peptides. Score 0.575 Taking the results from Round 4 Chains 32, Residues 210, Estimated correctness of the model 40.5 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6870 restraints for refining 3212 atoms. 5975 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2310 (Rfree = 0.000) for 3212 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 2: After refmac, R = 0.2162 (Rfree = 0.000) for 3189 atoms. Found 26 (28 requested) and removed 17 (14 requested) atoms. Cycle 3: After refmac, R = 0.2152 (Rfree = 0.000) for 3174 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 4: After refmac, R = 0.2083 (Rfree = 0.000) for 3169 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 5: After refmac, R = 0.2039 (Rfree = 0.000) for 3167 atoms. Found 21 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3260 seeds are put forward Round 1: 210 peptides, 33 chains. Longest chain 16 peptides. Score 0.476 Round 2: 243 peptides, 30 chains. Longest chain 20 peptides. Score 0.616 Round 3: 261 peptides, 37 chains. Longest chain 18 peptides. Score 0.580 Round 4: 254 peptides, 34 chains. Longest chain 22 peptides. Score 0.597 Round 5: 259 peptides, 34 chains. Longest chain 19 peptides. Score 0.611 Taking the results from Round 2 Chains 30, Residues 213, Estimated correctness of the model 45.3 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6981 restraints for refining 3168 atoms. 6079 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2196 (Rfree = 0.000) for 3168 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 7: After refmac, R = 0.2067 (Rfree = 0.000) for 3164 atoms. Found 12 (28 requested) and removed 19 (14 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 3147 atoms. Found 22 (28 requested) and removed 14 (14 requested) atoms. Cycle 9: After refmac, R = 0.2068 (Rfree = 0.000) for 3149 atoms. Found 16 (28 requested) and removed 15 (14 requested) atoms. Cycle 10: After refmac, R = 0.1998 (Rfree = 0.000) for 3150 atoms. Found 10 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.70 2.89 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3221 seeds are put forward Round 1: 233 peptides, 32 chains. Longest chain 20 peptides. Score 0.563 Round 2: 255 peptides, 33 chains. Longest chain 20 peptides. Score 0.612 Round 3: 249 peptides, 32 chains. Longest chain 21 peptides. Score 0.608 Round 4: 236 peptides, 30 chains. Longest chain 21 peptides. Score 0.597 Round 5: 248 peptides, 31 chains. Longest chain 21 peptides. Score 0.617 Taking the results from Round 5 Chains 31, Residues 217, Estimated correctness of the model 45.6 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6713 restraints for refining 3140 atoms. 5735 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2237 (Rfree = 0.000) for 3140 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 12: After refmac, R = 0.2095 (Rfree = 0.000) for 3137 atoms. Found 18 (28 requested) and removed 17 (14 requested) atoms. Cycle 13: After refmac, R = 0.1984 (Rfree = 0.000) for 3132 atoms. Found 14 (28 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.1903 (Rfree = 0.000) for 3125 atoms. Found 12 (28 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.1816 (Rfree = 0.000) for 3116 atoms. Found 9 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.62 2.80 Search for helices and strands: 0 residues in 0 chains, 3189 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3217 seeds are put forward Round 1: 230 peptides, 32 chains. Longest chain 19 peptides. Score 0.554 Round 2: 252 peptides, 33 chains. Longest chain 21 peptides. Score 0.604 Round 3: 253 peptides, 33 chains. Longest chain 21 peptides. Score 0.607 Round 4: 246 peptides, 28 chains. Longest chain 22 peptides. Score 0.647 Round 5: 251 peptides, 28 chains. Longest chain 24 peptides. Score 0.660 Taking the results from Round 5 Chains 28, Residues 223, Estimated correctness of the model 56.2 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6839 restraints for refining 3140 atoms. 5899 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2130 (Rfree = 0.000) for 3140 atoms. Found 27 (28 requested) and removed 18 (14 requested) atoms. Cycle 17: After refmac, R = 0.1975 (Rfree = 0.000) for 3140 atoms. Found 13 (28 requested) and removed 16 (14 requested) atoms. Cycle 18: After refmac, R = 0.1936 (Rfree = 0.000) for 3132 atoms. Found 11 (28 requested) and removed 14 (14 requested) atoms. Cycle 19: After refmac, R = 0.1918 (Rfree = 0.000) for 3128 atoms. Found 7 (28 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.1898 (Rfree = 0.000) for 3120 atoms. Found 11 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3221 seeds are put forward Round 1: 227 peptides, 32 chains. Longest chain 21 peptides. Score 0.545 Round 2: 241 peptides, 29 chains. Longest chain 19 peptides. Score 0.623 Round 3: 253 peptides, 30 chains. Longest chain 21 peptides. Score 0.642 Round 4: 250 peptides, 31 chains. Longest chain 16 peptides. Score 0.623 Round 5: 269 peptides, 30 chains. Longest chain 29 peptides. Score 0.680 Taking the results from Round 5 Chains 30, Residues 239, Estimated correctness of the model 60.8 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6699 restraints for refining 3162 atoms. 5693 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2120 (Rfree = 0.000) for 3162 atoms. Found 23 (28 requested) and removed 17 (14 requested) atoms. Cycle 22: After refmac, R = 0.1943 (Rfree = 0.000) for 3161 atoms. Found 11 (28 requested) and removed 15 (14 requested) atoms. Cycle 23: After refmac, R = 0.1873 (Rfree = 0.000) for 3147 atoms. Found 10 (28 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.1844 (Rfree = 0.000) for 3141 atoms. Found 7 (28 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.1828 (Rfree = 0.000) for 3129 atoms. Found 8 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 42 residues added (5 deleted due to clashes), 3220 seeds are put forward Round 1: 236 peptides, 32 chains. Longest chain 21 peptides. Score 0.572 Round 2: 244 peptides, 31 chains. Longest chain 19 peptides. Score 0.607 Round 3: 257 peptides, 36 chains. Longest chain 15 peptides. Score 0.581 Round 4: 260 peptides, 31 chains. Longest chain 32 peptides. Score 0.648 Round 5: 239 peptides, 33 chains. Longest chain 14 peptides. Score 0.567 Taking the results from Round 4 Chains 33, Residues 229, Estimated correctness of the model 53.4 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6599 restraints for refining 3160 atoms. 5548 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2135 (Rfree = 0.000) for 3160 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 27: After refmac, R = 0.1958 (Rfree = 0.000) for 3162 atoms. Found 14 (28 requested) and removed 15 (14 requested) atoms. Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 3158 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.1859 (Rfree = 0.000) for 3144 atoms. Found 12 (28 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.1831 (Rfree = 0.000) for 3136 atoms. Found 10 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3207 seeds are put forward Round 1: 234 peptides, 34 chains. Longest chain 20 peptides. Score 0.539 Round 2: 254 peptides, 33 chains. Longest chain 28 peptides. Score 0.609 Round 3: 264 peptides, 36 chains. Longest chain 19 peptides. Score 0.600 Round 4: 277 peptides, 32 chains. Longest chain 26 peptides. Score 0.678 Round 5: 249 peptides, 31 chains. Longest chain 19 peptides. Score 0.620 Taking the results from Round 4 Chains 34, Residues 245, Estimated correctness of the model 60.4 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6497 restraints for refining 3210 atoms. 5324 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 3210 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 32: After refmac, R = 0.1885 (Rfree = 0.000) for 3198 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 3188 atoms. Found 3 (28 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1841 (Rfree = 0.000) for 3175 atoms. Found 5 (28 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.1871 (Rfree = 0.000) for 3165 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3253 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3273 seeds are put forward Round 1: 217 peptides, 33 chains. Longest chain 18 peptides. Score 0.499 Round 2: 229 peptides, 30 chains. Longest chain 20 peptides. Score 0.577 Round 3: 225 peptides, 32 chains. Longest chain 28 peptides. Score 0.539 Round 4: 225 peptides, 31 chains. Longest chain 17 peptides. Score 0.552 Round 5: 227 peptides, 33 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 2 Chains 31, Residues 199, Estimated correctness of the model 34.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7276 restraints for refining 3202 atoms. 6449 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1995 (Rfree = 0.000) for 3202 atoms. Found 19 (28 requested) and removed 17 (14 requested) atoms. Cycle 37: After refmac, R = 0.1957 (Rfree = 0.000) for 3198 atoms. Found 15 (28 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.1888 (Rfree = 0.000) for 3197 atoms. Found 9 (28 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.1766 (Rfree = 0.000) for 3188 atoms. Found 11 (28 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1743 (Rfree = 0.000) for 3181 atoms. Found 5 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3270 seeds are put forward Round 1: 197 peptides, 32 chains. Longest chain 15 peptides. Score 0.446 Round 2: 213 peptides, 32 chains. Longest chain 15 peptides. Score 0.501 Round 3: 219 peptides, 29 chains. Longest chain 23 peptides. Score 0.561 Round 4: 217 peptides, 33 chains. Longest chain 17 peptides. Score 0.499 Round 5: 233 peptides, 35 chains. Longest chain 24 peptides. Score 0.523 Taking the results from Round 3 Chains 31, Residues 190, Estimated correctness of the model 30.1 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7236 restraints for refining 3212 atoms. 6401 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1962 (Rfree = 0.000) for 3212 atoms. Found 28 (28 requested) and removed 17 (14 requested) atoms. Cycle 42: After refmac, R = 0.1795 (Rfree = 0.000) for 3221 atoms. Found 6 (28 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.1773 (Rfree = 0.000) for 3206 atoms. Found 11 (28 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1704 (Rfree = 0.000) for 3202 atoms. Found 4 (28 requested) and removed 15 (14 requested) atoms. Cycle 45: After refmac, R = 0.1662 (Rfree = 0.000) for 3188 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3269 seeds are put forward Round 1: 176 peptides, 31 chains. Longest chain 12 peptides. Score 0.385 Round 2: 201 peptides, 31 chains. Longest chain 13 peptides. Score 0.475 Round 3: 211 peptides, 30 chains. Longest chain 15 peptides. Score 0.523 Round 4: 211 peptides, 32 chains. Longest chain 13 peptides. Score 0.494 Round 5: 211 peptides, 29 chains. Longest chain 15 peptides. Score 0.536 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 182, Estimated correctness of the model 22.7 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6759 reflections ( 98.21 % complete ) and 7344 restraints for refining 3207 atoms. 6610 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1893 (Rfree = 0.000) for 3207 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1799 (Rfree = 0.000) for 3190 atoms. Found 0 (28 requested) and removed 5 (14 requested) atoms. Cycle 48: After refmac, R = 0.1775 (Rfree = 0.000) for 3184 atoms. Found 0 (28 requested) and removed 3 (14 requested) atoms. Cycle 49: After refmac, R = 0.1758 (Rfree = 0.000) for 3181 atoms. Found 0 (28 requested) and removed 0 (14 requested) atoms. Writing output files ... TimeTaking 41.15