Sun 23 Dec 22:22:44 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 1vlm-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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/1vlm-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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 22:22:53 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/1vlm-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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 316 and 0 Target number of residues in the AU: 316 Target solvent content: 0.6079 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.2-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.65 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: 93.922 3.200 Wilson plot Bfac: 55.83 7616 reflections ( 99.75 % complete ) and 0 restraints for refining 3914 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3114 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2581 (Rfree = 0.000) for 3914 atoms. Found 35 (35 requested) and removed 54 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.22 Search for helices and strands: 0 residues in 0 chains, 3965 seeds are put forward NCS extension: 0 residues added, 3965 seeds are put forward Round 1: 207 peptides, 38 chains. Longest chain 18 peptides. Score 0.387 Round 2: 258 peptides, 37 chains. Longest chain 25 peptides. Score 0.567 Round 3: 267 peptides, 34 chains. Longest chain 20 peptides. Score 0.627 Round 4: 282 peptides, 30 chains. Longest chain 36 peptides. Score 0.704 Round 5: 281 peptides, 32 chains. Longest chain 24 peptides. Score 0.682 Taking the results from Round 4 Chains 30, Residues 252, Estimated correctness of the model 66.0 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 76 A 29 chains (254 residues) following loop building 1 chains (53 residues) in sequence following loop building ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6397 restraints for refining 3199 atoms. 5203 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2710 (Rfree = 0.000) for 3199 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 3147 atoms. Found 13 (27 requested) and removed 24 (14 requested) atoms. Cycle 3: After refmac, R = 0.2510 (Rfree = 0.000) for 3124 atoms. Found 6 (27 requested) and removed 16 (14 requested) atoms. Cycle 4: After refmac, R = 0.2449 (Rfree = 0.000) for 3104 atoms. Found 8 (25 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.2423 (Rfree = 0.000) for 3093 atoms. Found 3 (25 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.23 Search for helices and strands: 0 residues in 0 chains, 3169 seeds are put forward NCS extension: 112 residues added (19 deleted due to clashes), 3281 seeds are put forward Round 1: 250 peptides, 35 chains. Longest chain 33 peptides. Score 0.570 Round 2: 273 peptides, 27 chains. Longest chain 51 peptides. Score 0.715 Round 3: 289 peptides, 32 chains. Longest chain 39 peptides. Score 0.700 Round 4: 277 peptides, 30 chains. Longest chain 36 peptides. Score 0.694 Round 5: 286 peptides, 33 chains. Longest chain 37 peptides. Score 0.683 Taking the results from Round 2 Chains 30, Residues 246, Estimated correctness of the model 68.3 % 6 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 54 A and 59 A 28 chains (252 residues) following loop building 4 chains (92 residues) in sequence following loop building ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6013 restraints for refining 3199 atoms. 4658 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2658 (Rfree = 0.000) for 3199 atoms. Found 25 (25 requested) and removed 40 (14 requested) atoms. Cycle 7: After refmac, R = 0.2548 (Rfree = 0.000) for 3163 atoms. Found 25 (25 requested) and removed 26 (14 requested) atoms. Cycle 8: After refmac, R = 0.2458 (Rfree = 0.000) for 3147 atoms. Found 14 (24 requested) and removed 19 (14 requested) atoms. Cycle 9: After refmac, R = 0.2371 (Rfree = 0.000) for 3138 atoms. Found 14 (24 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 3123 atoms. Found 14 (23 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.22 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 3263 seeds are put forward Round 1: 253 peptides, 35 chains. Longest chain 31 peptides. Score 0.578 Round 2: 272 peptides, 27 chains. Longest chain 35 peptides. Score 0.713 Round 3: 278 peptides, 26 chains. Longest chain 34 peptides. Score 0.734 Round 4: 288 peptides, 27 chains. Longest chain 27 peptides. Score 0.744 Round 5: 264 peptides, 26 chains. Longest chain 40 peptides. Score 0.706 Taking the results from Round 4 Chains 30, Residues 261, Estimated correctness of the model 74.0 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 30 chains (261 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6445 restraints for refining 3199 atoms. 5206 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2522 (Rfree = 0.000) for 3199 atoms. Found 22 (22 requested) and removed 24 (14 requested) atoms. Cycle 12: After refmac, R = 0.2331 (Rfree = 0.000) for 3182 atoms. Found 10 (22 requested) and removed 16 (14 requested) atoms. Cycle 13: After refmac, R = 0.2346 (Rfree = 0.000) for 3171 atoms. Found 16 (21 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.2306 (Rfree = 0.000) for 3166 atoms. Found 17 (21 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2272 (Rfree = 0.000) for 3164 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.23 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3276 seeds are put forward Round 1: 227 peptides, 30 chains. Longest chain 18 peptides. Score 0.567 Round 2: 261 peptides, 27 chains. Longest chain 46 peptides. Score 0.689 Round 3: 272 peptides, 28 chains. Longest chain 18 peptides. Score 0.703 Round 4: 265 peptides, 28 chains. Longest chain 39 peptides. Score 0.688 Round 5: 285 peptides, 31 chains. Longest chain 20 peptides. Score 0.701 Taking the results from Round 3 Chains 30, Residues 244, Estimated correctness of the model 65.8 % 5 chains (54 residues) have been docked in sequence Building loops using Loopy2018 30 chains (244 residues) following loop building 5 chains (54 residues) in sequence following loop building ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6582 restraints for refining 3199 atoms. 5437 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2521 (Rfree = 0.000) for 3199 atoms. Found 20 (20 requested) and removed 46 (14 requested) atoms. Cycle 17: After refmac, R = 0.2404 (Rfree = 0.000) for 3159 atoms. Found 15 (19 requested) and removed 20 (14 requested) atoms. Cycle 18: After refmac, R = 0.2337 (Rfree = 0.000) for 3148 atoms. Found 7 (18 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2270 (Rfree = 0.000) for 3135 atoms. Found 5 (18 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2242 (Rfree = 0.000) for 3124 atoms. Found 6 (17 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3208 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 3220 seeds are put forward Round 1: 227 peptides, 34 chains. Longest chain 28 peptides. Score 0.514 Round 2: 256 peptides, 28 chains. Longest chain 27 peptides. Score 0.667 Round 3: 258 peptides, 33 chains. Longest chain 22 peptides. Score 0.616 Round 4: 273 peptides, 33 chains. Longest chain 24 peptides. Score 0.653 Round 5: 260 peptides, 34 chains. Longest chain 19 peptides. Score 0.609 Taking the results from Round 2 Chains 28, Residues 228, Estimated correctness of the model 57.9 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6605 restraints for refining 3199 atoms. 5525 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 3199 atoms. Found 17 (17 requested) and removed 22 (14 requested) atoms. Cycle 22: After refmac, R = 0.2258 (Rfree = 0.000) for 3184 atoms. Found 11 (17 requested) and removed 16 (14 requested) atoms. Cycle 23: After refmac, R = 0.2184 (Rfree = 0.000) for 3173 atoms. Found 8 (17 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2102 (Rfree = 0.000) for 3165 atoms. Found 3 (17 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2095 (Rfree = 0.000) for 3152 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3248 seeds are put forward Round 1: 227 peptides, 36 chains. Longest chain 18 peptides. Score 0.486 Round 2: 248 peptides, 31 chains. Longest chain 18 peptides. Score 0.613 Round 3: 245 peptides, 30 chains. Longest chain 20 peptides. Score 0.617 Round 4: 247 peptides, 29 chains. Longest chain 22 peptides. Score 0.634 Round 5: 243 peptides, 28 chains. Longest chain 24 peptides. Score 0.635 Taking the results from Round 5 Chains 29, Residues 215, Estimated correctness of the model 50.2 % 3 chains (54 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6604 restraints for refining 3199 atoms. 5545 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2409 (Rfree = 0.000) for 3199 atoms. Found 17 (17 requested) and removed 22 (14 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 3180 atoms. Found 15 (17 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.2184 (Rfree = 0.000) for 3178 atoms. Found 12 (17 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.2115 (Rfree = 0.000) for 3166 atoms. Found 10 (17 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2044 (Rfree = 0.000) for 3157 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3255 seeds are put forward Round 1: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.432 Round 2: 227 peptides, 29 chains. Longest chain 24 peptides. Score 0.580 Round 3: 224 peptides, 30 chains. Longest chain 25 peptides. Score 0.558 Round 4: 223 peptides, 31 chains. Longest chain 20 peptides. Score 0.542 Round 5: 235 peptides, 31 chains. Longest chain 20 peptides. Score 0.577 Taking the results from Round 2 Chains 31, Residues 198, Estimated correctness of the model 35.6 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 7036 restraints for refining 3198 atoms. 6132 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2236 (Rfree = 0.000) for 3198 atoms. Found 17 (17 requested) and removed 24 (14 requested) atoms. Cycle 32: After refmac, R = 0.2123 (Rfree = 0.000) for 3185 atoms. Found 7 (17 requested) and removed 15 (14 requested) atoms. Cycle 33: After refmac, R = 0.2105 (Rfree = 0.000) for 3175 atoms. Found 9 (17 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2067 (Rfree = 0.000) for 3167 atoms. Found 8 (17 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2004 (Rfree = 0.000) for 3160 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.24 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3251 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 13 peptides. Score 0.369 Round 2: 230 peptides, 33 chains. Longest chain 24 peptides. Score 0.537 Round 3: 210 peptides, 30 chains. Longest chain 13 peptides. Score 0.516 Round 4: 213 peptides, 29 chains. Longest chain 18 peptides. Score 0.539 Round 5: 217 peptides, 28 chains. Longest chain 27 peptides. Score 0.564 Taking the results from Round 5 Chains 28, Residues 189, Estimated correctness of the model 31.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 7244 restraints for refining 3199 atoms. 6482 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 3199 atoms. Found 17 (17 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.2063 (Rfree = 0.000) for 3195 atoms. Found 7 (17 requested) and removed 16 (14 requested) atoms. Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 3184 atoms. Found 8 (17 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.1870 (Rfree = 0.000) for 3177 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1851 (Rfree = 0.000) for 3169 atoms. Found 4 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.23 Search for helices and strands: 0 residues in 0 chains, 3238 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 3276 seeds are put forward Round 1: 201 peptides, 36 chains. Longest chain 11 peptides. Score 0.396 Round 2: 225 peptides, 30 chains. Longest chain 16 peptides. Score 0.561 Round 3: 225 peptides, 33 chains. Longest chain 16 peptides. Score 0.521 Round 4: 225 peptides, 35 chains. Longest chain 15 peptides. Score 0.494 Round 5: 236 peptides, 35 chains. Longest chain 20 peptides. Score 0.528 Taking the results from Round 2 Chains 30, Residues 195, Estimated correctness of the model 30.1 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6962 restraints for refining 3199 atoms. 6126 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 3199 atoms. Found 17 (17 requested) and removed 29 (14 requested) atoms. Cycle 42: After refmac, R = 0.2007 (Rfree = 0.000) for 3180 atoms. Found 15 (17 requested) and removed 17 (14 requested) atoms. Cycle 43: After refmac, R = 0.1999 (Rfree = 0.000) for 3173 atoms. Found 10 (17 requested) and removed 17 (14 requested) atoms. Cycle 44: After refmac, R = 0.1925 (Rfree = 0.000) for 3161 atoms. Found 10 (17 requested) and removed 15 (14 requested) atoms. Cycle 45: After refmac, R = 0.1879 (Rfree = 0.000) for 3153 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3244 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 16 peptides. Score 0.402 Round 2: 216 peptides, 32 chains. Longest chain 17 peptides. Score 0.507 Round 3: 214 peptides, 32 chains. Longest chain 15 peptides. Score 0.500 Round 4: 224 peptides, 31 chains. Longest chain 15 peptides. Score 0.545 Round 5: 227 peptides, 31 chains. Longest chain 15 peptides. Score 0.554 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 196, Estimated correctness of the model 28.1 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vlm-3_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (196 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7616 reflections ( 99.75 % complete ) and 6999 restraints for refining 3199 atoms. 6169 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2191 (Rfree = 0.000) for 3199 atoms. Found 0 (17 requested) and removed 6 (14 requested) atoms. Cycle 47: After refmac, R = 0.2151 (Rfree = 0.000) for 3188 atoms. Found 0 (17 requested) and removed 3 (14 requested) atoms. Cycle 48: After refmac, R = 0.2092 (Rfree = 0.000) for 3182 atoms. Found 0 (17 requested) and removed 5 (14 requested) atoms. Cycle 49: After refmac, R = 0.2070 (Rfree = 0.000) for 3173 atoms. TimeTaking 54.68