Mon 24 Dec 07:56:25 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-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-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-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-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 07:56:30 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-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-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 392 and 0 Target number of residues in the AU: 392 Target solvent content: 0.5070 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-3.0-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-3.0-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 3.000 Wilson plot Bfac: 24.83 8199 reflections ( 98.22 % complete ) and 0 restraints for refining 3896 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2913 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2405 (Rfree = 0.000) for 3896 atoms. Found 38 (42 requested) and removed 45 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.38 2.54 Search for helices and strands: 0 residues in 0 chains, 3928 seeds are put forward NCS extension: 0 residues added, 3928 seeds are put forward Round 1: 195 peptides, 38 chains. Longest chain 9 peptides. Score 0.345 Round 2: 221 peptides, 37 chains. Longest chain 12 peptides. Score 0.455 Round 3: 256 peptides, 37 chains. Longest chain 15 peptides. Score 0.566 Round 4: 263 peptides, 38 chains. Longest chain 25 peptides. Score 0.573 Round 5: 266 peptides, 34 chains. Longest chain 26 peptides. Score 0.629 Taking the results from Round 5 Chains 38, Residues 232, Estimated correctness of the model 58.1 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6484 restraints for refining 3229 atoms. 5464 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2931 (Rfree = 0.000) for 3229 atoms. Found 34 (34 requested) and removed 53 (17 requested) atoms. Cycle 2: After refmac, R = 0.2300 (Rfree = 0.000) for 3176 atoms. Found 25 (34 requested) and removed 23 (17 requested) atoms. Cycle 3: After refmac, R = 0.2175 (Rfree = 0.000) for 3154 atoms. Found 17 (34 requested) and removed 17 (17 requested) atoms. Cycle 4: After refmac, R = 0.2083 (Rfree = 0.000) for 3144 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. Cycle 5: After refmac, R = 0.2061 (Rfree = 0.000) for 3132 atoms. Found 18 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.56 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3246 seeds are put forward Round 1: 236 peptides, 35 chains. Longest chain 18 peptides. Score 0.532 Round 2: 264 peptides, 27 chains. Longest chain 40 peptides. Score 0.700 Round 3: 273 peptides, 32 chains. Longest chain 21 peptides. Score 0.669 Round 4: 264 peptides, 30 chains. Longest chain 28 peptides. Score 0.669 Round 5: 273 peptides, 29 chains. Longest chain 28 peptides. Score 0.700 Taking the results from Round 5 Chains 29, Residues 244, Estimated correctness of the model 71.6 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6367 restraints for refining 3187 atoms. 5295 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2646 (Rfree = 0.000) for 3187 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 7: After refmac, R = 0.2316 (Rfree = 0.000) for 3171 atoms. Found 22 (34 requested) and removed 24 (17 requested) atoms. Cycle 8: After refmac, R = 0.2159 (Rfree = 0.000) for 3160 atoms. Found 22 (34 requested) and removed 18 (17 requested) atoms. Cycle 9: After refmac, R = 0.1959 (Rfree = 0.000) for 3155 atoms. Found 6 (34 requested) and removed 18 (17 requested) atoms. Cycle 10: After refmac, R = 0.2024 (Rfree = 0.000) for 3135 atoms. Found 15 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.40 2.57 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 3239 seeds are put forward Round 1: 252 peptides, 33 chains. Longest chain 17 peptides. Score 0.604 Round 2: 276 peptides, 30 chains. Longest chain 31 peptides. Score 0.696 Round 3: 279 peptides, 29 chains. Longest chain 45 peptides. Score 0.712 Round 4: 286 peptides, 29 chains. Longest chain 32 peptides. Score 0.726 Round 5: 281 peptides, 25 chains. Longest chain 48 peptides. Score 0.753 Taking the results from Round 5 Chains 25, Residues 256, Estimated correctness of the model 80.1 % 3 chains (86 residues) have been docked in sequence Building loops using Loopy2018 25 chains (256 residues) following loop building 3 chains (86 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5857 restraints for refining 3210 atoms. 4487 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2748 (Rfree = 0.000) for 3210 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 12: After refmac, R = 0.2164 (Rfree = 0.000) for 3195 atoms. Found 23 (33 requested) and removed 20 (17 requested) atoms. Cycle 13: After refmac, R = 0.2159 (Rfree = 0.000) for 3190 atoms. Found 16 (33 requested) and removed 18 (17 requested) atoms. Cycle 14: After refmac, R = 0.2024 (Rfree = 0.000) for 3184 atoms. Found 11 (32 requested) and removed 18 (17 requested) atoms. Cycle 15: After refmac, R = 0.1965 (Rfree = 0.000) for 3174 atoms. Found 12 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.39 2.56 Search for helices and strands: 0 residues in 0 chains, 3230 seeds are put forward NCS extension: 79 residues added (5 deleted due to clashes), 3309 seeds are put forward Round 1: 254 peptides, 27 chains. Longest chain 33 peptides. Score 0.678 Round 2: 281 peptides, 27 chains. Longest chain 45 peptides. Score 0.735 Round 3: 284 peptides, 28 chains. Longest chain 42 peptides. Score 0.732 Round 4: 286 peptides, 29 chains. Longest chain 38 peptides. Score 0.726 Round 5: 258 peptides, 29 chains. Longest chain 24 peptides. Score 0.666 Taking the results from Round 2 Chains 29, Residues 254, Estimated correctness of the model 77.4 % 4 chains (88 residues) have been docked in sequence Building loops using Loopy2018 29 chains (254 residues) following loop building 4 chains (88 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5982 restraints for refining 3228 atoms. 4590 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2365 (Rfree = 0.000) for 3228 atoms. Found 22 (31 requested) and removed 32 (17 requested) atoms. Cycle 17: After refmac, R = 0.2024 (Rfree = 0.000) for 3206 atoms. Found 14 (30 requested) and removed 20 (17 requested) atoms. Cycle 18: After refmac, R = 0.1972 (Rfree = 0.000) for 3195 atoms. Found 5 (29 requested) and removed 18 (17 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1913 (Rfree = 0.000) for 3180 atoms. Found 12 (29 requested) and removed 18 (17 requested) atoms. Cycle 20: After refmac, R = 0.1940 (Rfree = 0.000) for 3173 atoms. Found 9 (28 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.38 2.54 Search for helices and strands: 0 residues in 0 chains, 3247 seeds are put forward NCS extension: 34 residues added (5 deleted due to clashes), 3281 seeds are put forward Round 1: 262 peptides, 27 chains. Longest chain 33 peptides. Score 0.696 Round 2: 270 peptides, 25 chains. Longest chain 47 peptides. Score 0.732 Round 3: 266 peptides, 27 chains. Longest chain 47 peptides. Score 0.705 Round 4: 262 peptides, 25 chains. Longest chain 40 peptides. Score 0.716 Round 5: 265 peptides, 30 chains. Longest chain 25 peptides. Score 0.671 Taking the results from Round 2 Chains 27, Residues 245, Estimated correctness of the model 76.9 % 4 chains (75 residues) have been docked in sequence Building loops using Loopy2018 27 chains (245 residues) following loop building 4 chains (75 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6092 restraints for refining 3221 atoms. 4799 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2164 (Rfree = 0.000) for 3221 atoms. Found 23 (27 requested) and removed 26 (17 requested) atoms. Cycle 22: After refmac, R = 0.1968 (Rfree = 0.000) for 3212 atoms. Found 6 (27 requested) and removed 17 (17 requested) atoms. Cycle 23: After refmac, R = 0.1917 (Rfree = 0.000) for 3194 atoms. Found 8 (26 requested) and removed 18 (17 requested) atoms. Cycle 24: After refmac, R = 0.1893 (Rfree = 0.000) for 3184 atoms. Found 6 (25 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 3171 atoms. Found 9 (24 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.39 2.56 Search for helices and strands: 0 residues in 0 chains, 3248 seeds are put forward NCS extension: 55 residues added (14 deleted due to clashes), 3303 seeds are put forward Round 1: 248 peptides, 28 chains. Longest chain 38 peptides. Score 0.652 Round 2: 263 peptides, 28 chains. Longest chain 23 peptides. Score 0.688 Round 3: 265 peptides, 28 chains. Longest chain 41 peptides. Score 0.692 Round 4: 258 peptides, 28 chains. Longest chain 31 peptides. Score 0.676 Round 5: 268 peptides, 31 chains. Longest chain 24 peptides. Score 0.667 Taking the results from Round 3 Chains 30, Residues 237, Estimated correctness of the model 70.2 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6409 restraints for refining 3231 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 3231 atoms. Found 22 (24 requested) and removed 23 (17 requested) atoms. Cycle 27: After refmac, R = 0.1958 (Rfree = 0.000) for 3223 atoms. Found 11 (24 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.1898 (Rfree = 0.000) for 3213 atoms. Found 15 (24 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.1910 (Rfree = 0.000) for 3208 atoms. Found 13 (24 requested) and removed 19 (17 requested) atoms. Cycle 30: After refmac, R = 0.1793 (Rfree = 0.000) for 3196 atoms. Found 14 (24 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.39 2.56 Search for helices and strands: 0 residues in 0 chains, 3267 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 3302 seeds are put forward Round 1: 243 peptides, 28 chains. Longest chain 20 peptides. Score 0.640 Round 2: 257 peptides, 25 chains. Longest chain 23 peptides. Score 0.706 Round 3: 262 peptides, 25 chains. Longest chain 35 peptides. Score 0.716 Round 4: 269 peptides, 26 chains. Longest chain 43 peptides. Score 0.721 Round 5: 264 peptides, 25 chains. Longest chain 35 peptides. Score 0.720 Taking the results from Round 4 Chains 27, Residues 243, Estimated correctness of the model 75.1 % 2 chains (55 residues) have been docked in sequence Building loops using Loopy2018 27 chains (243 residues) following loop building 2 chains (55 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6369 restraints for refining 3231 atoms. 5172 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2131 (Rfree = 0.000) for 3231 atoms. Found 24 (24 requested) and removed 19 (17 requested) atoms. Cycle 32: After refmac, R = 0.1926 (Rfree = 0.000) for 3234 atoms. Found 9 (23 requested) and removed 18 (17 requested) atoms. Cycle 33: After refmac, R = 0.1844 (Rfree = 0.000) for 3222 atoms. Found 11 (22 requested) and removed 18 (17 requested) atoms. Cycle 34: After refmac, R = 0.1849 (Rfree = 0.000) for 3213 atoms. Found 10 (22 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1812 (Rfree = 0.000) for 3204 atoms. Found 9 (21 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.38 2.54 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 60 residues added (1 deleted due to clashes), 3303 seeds are put forward Round 1: 252 peptides, 28 chains. Longest chain 21 peptides. Score 0.662 Round 2: 259 peptides, 24 chains. Longest chain 33 peptides. Score 0.720 Round 3: 269 peptides, 25 chains. Longest chain 23 peptides. Score 0.730 Round 4: 249 peptides, 26 chains. Longest chain 40 peptides. Score 0.677 Round 5: 251 peptides, 26 chains. Longest chain 19 peptides. Score 0.682 Taking the results from Round 3 Chains 29, Residues 244, Estimated correctness of the model 76.6 % 3 chains (39 residues) have been docked in sequence Building loops using Loopy2018 29 chains (244 residues) following loop building 3 chains (39 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6474 restraints for refining 3231 atoms. 5375 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2067 (Rfree = 0.000) for 3231 atoms. Found 20 (20 requested) and removed 21 (17 requested) atoms. Cycle 37: After refmac, R = 0.1955 (Rfree = 0.000) for 3222 atoms. Found 18 (20 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.1902 (Rfree = 0.000) for 3216 atoms. Found 8 (19 requested) and removed 18 (17 requested) atoms. Cycle 39: After refmac, R = 0.1804 (Rfree = 0.000) for 3200 atoms. Found 10 (18 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1727 (Rfree = 0.000) for 3187 atoms. Found 11 (18 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.36 2.52 Search for helices and strands: 0 residues in 0 chains, 3261 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3286 seeds are put forward Round 1: 235 peptides, 27 chains. Longest chain 19 peptides. Score 0.631 Round 2: 253 peptides, 28 chains. Longest chain 25 peptides. Score 0.665 Round 3: 249 peptides, 28 chains. Longest chain 16 peptides. Score 0.655 Round 4: 245 peptides, 25 chains. Longest chain 29 peptides. Score 0.679 Round 5: 251 peptides, 26 chains. Longest chain 23 peptides. Score 0.682 Taking the results from Round 5 Chains 28, Residues 225, Estimated correctness of the model 68.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6761 restraints for refining 3205 atoms. 5832 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2270 (Rfree = 0.000) for 3205 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.1825 (Rfree = 0.000) for 3196 atoms. Found 10 (17 requested) and removed 18 (17 requested) atoms. Cycle 43: After refmac, R = 0.1774 (Rfree = 0.000) for 3186 atoms. Found 6 (17 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 3175 atoms. Found 6 (17 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1760 (Rfree = 0.000) for 3161 atoms. Found 8 (17 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.37 2.53 Search for helices and strands: 0 residues in 0 chains, 3227 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3256 seeds are put forward Round 1: 213 peptides, 30 chains. Longest chain 17 peptides. Score 0.529 Round 2: 250 peptides, 29 chains. Longest chain 24 peptides. Score 0.646 Round 3: 223 peptides, 25 chains. Longest chain 18 peptides. Score 0.624 Round 4: 233 peptides, 22 chains. Longest chain 21 peptides. Score 0.684 Round 5: 225 peptides, 24 chains. Longest chain 18 peptides. Score 0.641 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 211, Estimated correctness of the model 68.8 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8199 reflections ( 98.22 % complete ) and 6846 restraints for refining 3199 atoms. 5974 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1928 (Rfree = 0.000) for 3199 atoms. Found 0 (17 requested) and removed 16 (17 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 3180 atoms. Found 0 (17 requested) and removed 8 (17 requested) atoms. Cycle 48: After refmac, R = 0.1860 (Rfree = 0.000) for 3172 atoms. Found 0 (17 requested) and removed 4 (17 requested) atoms. Cycle 49: After refmac, R = 0.1811 (Rfree = 0.000) for 3168 atoms. TimeTaking 45.23