Sun 23 Dec 22:23:10 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 2p97-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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/2p97-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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 22:23:19 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/2p97-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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 347 and 0 Target number of residues in the AU: 347 Target solvent content: 0.6324 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.6-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.85 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: 72.889 3.600 Wilson plot Bfac: 67.66 6389 reflections ( 99.72 % complete ) and 0 restraints for refining 3589 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3083 (Rfree = 0.000) for 3589 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 3658 seeds are put forward NCS extension: 0 residues added, 3658 seeds are put forward Round 1: 221 peptides, 36 chains. Longest chain 12 peptides. Score 0.434 Round 2: 258 peptides, 30 chains. Longest chain 24 peptides. Score 0.605 Round 3: 275 peptides, 28 chains. Longest chain 24 peptides. Score 0.663 Round 4: 267 peptides, 27 chains. Longest chain 33 peptides. Score 0.656 Round 5: 265 peptides, 27 chains. Longest chain 26 peptides. Score 0.651 Taking the results from Round 3 Chains 29, Residues 247, Estimated correctness of the model 37.6 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6071 restraints for refining 2916 atoms. 5019 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2764 (Rfree = 0.000) for 2916 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. Cycle 2: After refmac, R = 0.2520 (Rfree = 0.000) for 2888 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 3: After refmac, R = 0.2534 (Rfree = 0.000) for 2873 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2384 (Rfree = 0.000) for 2860 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2556 (Rfree = 0.000) for 2846 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 2947 seeds are put forward Round 1: 259 peptides, 31 chains. Longest chain 24 peptides. Score 0.596 Round 2: 261 peptides, 30 chains. Longest chain 33 peptides. Score 0.612 Round 3: 278 peptides, 25 chains. Longest chain 45 peptides. Score 0.697 Round 4: 282 peptides, 26 chains. Longest chain 36 peptides. Score 0.695 Round 5: 273 peptides, 32 chains. Longest chain 25 peptides. Score 0.618 Taking the results from Round 3 Chains 25, Residues 253, Estimated correctness of the model 48.7 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6249 restraints for refining 2915 atoms. 5182 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2675 (Rfree = 0.000) for 2915 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 7: After refmac, R = 0.2439 (Rfree = 0.000) for 2903 atoms. Found 6 (18 requested) and removed 15 (9 requested) atoms. Cycle 8: After refmac, R = 0.2361 (Rfree = 0.000) for 2881 atoms. Found 13 (18 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2247 (Rfree = 0.000) for 2875 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2226 (Rfree = 0.000) for 2861 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 59 residues added (16 deleted due to clashes), 3009 seeds are put forward Round 1: 261 peptides, 34 chains. Longest chain 29 peptides. Score 0.568 Round 2: 278 peptides, 29 chains. Longest chain 25 peptides. Score 0.659 Round 3: 276 peptides, 33 chains. Longest chain 27 peptides. Score 0.615 Round 4: 291 peptides, 32 chains. Longest chain 31 peptides. Score 0.657 Round 5: 287 peptides, 24 chains. Longest chain 39 peptides. Score 0.722 Taking the results from Round 5 Chains 26, Residues 263, Estimated correctness of the model 56.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6074 restraints for refining 2916 atoms. 5016 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2399 (Rfree = 0.000) for 2916 atoms. Found 11 (18 requested) and removed 14 (9 requested) atoms. Cycle 12: After refmac, R = 0.2257 (Rfree = 0.000) for 2885 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 2873 atoms. Found 4 (17 requested) and removed 12 (9 requested) atoms. Cycle 14: After refmac, R = 0.2172 (Rfree = 0.000) for 2861 atoms. Found 4 (17 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 2854 atoms. Found 9 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 37 residues added (17 deleted due to clashes), 2967 seeds are put forward Round 1: 230 peptides, 35 chains. Longest chain 24 peptides. Score 0.473 Round 2: 273 peptides, 32 chains. Longest chain 23 peptides. Score 0.618 Round 3: 292 peptides, 29 chains. Longest chain 50 peptides. Score 0.687 Round 4: 273 peptides, 29 chains. Longest chain 29 peptides. Score 0.649 Round 5: 288 peptides, 34 chains. Longest chain 31 peptides. Score 0.631 Taking the results from Round 3 Chains 31, Residues 263, Estimated correctness of the model 45.5 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 5928 restraints for refining 2916 atoms. 4789 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2462 (Rfree = 0.000) for 2916 atoms. Found 16 (16 requested) and removed 15 (9 requested) atoms. Cycle 17: After refmac, R = 0.2365 (Rfree = 0.000) for 2900 atoms. Found 13 (16 requested) and removed 15 (9 requested) atoms. Cycle 18: After refmac, R = 0.2235 (Rfree = 0.000) for 2891 atoms. Found 9 (16 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2126 (Rfree = 0.000) for 2880 atoms. Found 7 (16 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.2070 (Rfree = 0.000) for 2869 atoms. Found 8 (16 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2953 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2981 seeds are put forward Round 1: 231 peptides, 37 chains. Longest chain 15 peptides. Score 0.450 Round 2: 262 peptides, 33 chains. Longest chain 23 peptides. Score 0.582 Round 3: 263 peptides, 33 chains. Longest chain 17 peptides. Score 0.584 Round 4: 270 peptides, 32 chains. Longest chain 24 peptides. Score 0.611 Round 5: 260 peptides, 30 chains. Longest chain 33 peptides. Score 0.609 Taking the results from Round 4 Chains 34, Residues 238, Estimated correctness of the model 18.9 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6165 restraints for refining 2916 atoms. 5142 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2438 (Rfree = 0.000) for 2916 atoms. Found 16 (16 requested) and removed 12 (9 requested) atoms. Cycle 22: After refmac, R = 0.2182 (Rfree = 0.000) for 2900 atoms. Found 11 (16 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.2089 (Rfree = 0.000) for 2888 atoms. Found 7 (16 requested) and removed 12 (9 requested) atoms. Cycle 24: After refmac, R = 0.2208 (Rfree = 0.000) for 2875 atoms. Found 3 (16 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2345 (Rfree = 0.000) for 2866 atoms. Found 14 (16 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 2999 seeds are put forward Round 1: 253 peptides, 39 chains. Longest chain 15 peptides. Score 0.489 Round 2: 273 peptides, 32 chains. Longest chain 36 peptides. Score 0.618 Round 3: 268 peptides, 30 chains. Longest chain 34 peptides. Score 0.628 Round 4: 283 peptides, 31 chains. Longest chain 27 peptides. Score 0.650 Round 5: 285 peptides, 35 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 4 Chains 32, Residues 252, Estimated correctness of the model 33.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6285 restraints for refining 2915 atoms. 5276 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2527 (Rfree = 0.000) for 2915 atoms. Found 16 (16 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.2398 (Rfree = 0.000) for 2908 atoms. Found 5 (16 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2216 (Rfree = 0.000) for 2896 atoms. Found 7 (16 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2212 (Rfree = 0.000) for 2889 atoms. Found 2 (16 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2185 (Rfree = 0.000) for 2882 atoms. Found 2 (16 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 40 residues added (5 deleted due to clashes), 2982 seeds are put forward Round 1: 239 peptides, 36 chains. Longest chain 24 peptides. Score 0.486 Round 2: 262 peptides, 34 chains. Longest chain 31 peptides. Score 0.571 Round 3: 265 peptides, 36 chains. Longest chain 19 peptides. Score 0.556 Round 4: 278 peptides, 33 chains. Longest chain 20 peptides. Score 0.619 Round 5: 272 peptides, 32 chains. Longest chain 33 peptides. Score 0.616 Taking the results from Round 4 Chains 33, Residues 245, Estimated correctness of the model 21.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6443 restraints for refining 2916 atoms. 5496 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2554 (Rfree = 0.000) for 2916 atoms. Found 12 (16 requested) and removed 10 (9 requested) atoms. Cycle 32: After refmac, R = 0.2319 (Rfree = 0.000) for 2904 atoms. Found 8 (16 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2278 (Rfree = 0.000) for 2900 atoms. Found 2 (16 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2182 (Rfree = 0.000) for 2889 atoms. Found 2 (16 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2151 (Rfree = 0.000) for 2882 atoms. Found 1 (16 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 2938 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2966 seeds are put forward Round 1: 224 peptides, 36 chains. Longest chain 14 peptides. Score 0.443 Round 2: 246 peptides, 29 chains. Longest chain 22 peptides. Score 0.587 Round 3: 234 peptides, 30 chains. Longest chain 22 peptides. Score 0.545 Round 4: 239 peptides, 32 chains. Longest chain 19 peptides. Score 0.535 Round 5: 241 peptides, 31 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 2 Chains 30, Residues 217, Estimated correctness of the model 9.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6365 restraints for refining 2916 atoms. 5483 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2306 (Rfree = 0.000) for 2916 atoms. Found 5 (16 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2288 (Rfree = 0.000) for 2901 atoms. Found 13 (16 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2435 (Rfree = 0.000) for 2893 atoms. Found 14 (16 requested) and removed 31 (9 requested) atoms. Cycle 39: After refmac, R = 0.2244 (Rfree = 0.000) for 2868 atoms. Found 16 (16 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.2243 (Rfree = 0.000) for 2871 atoms. Found 13 (16 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2934 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2959 seeds are put forward Round 1: 221 peptides, 36 chains. Longest chain 13 peptides. Score 0.434 Round 2: 226 peptides, 30 chains. Longest chain 24 peptides. Score 0.524 Round 3: 213 peptides, 27 chains. Longest chain 13 peptides. Score 0.526 Round 4: 248 peptides, 28 chains. Longest chain 26 peptides. Score 0.603 Round 5: 244 peptides, 30 chains. Longest chain 26 peptides. Score 0.571 Taking the results from Round 4 Chains 29, Residues 220, Estimated correctness of the model 15.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6513 restraints for refining 2915 atoms. 5631 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2527 (Rfree = 0.000) for 2915 atoms. Found 13 (16 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 2905 atoms. Found 13 (16 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.2273 (Rfree = 0.000) for 2901 atoms. Found 16 (16 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.2258 (Rfree = 0.000) for 2895 atoms. Found 16 (16 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.2096 (Rfree = 0.000) for 2894 atoms. Found 16 (16 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3007 seeds are put forward Round 1: 187 peptides, 36 chains. Longest chain 13 peptides. Score 0.324 Round 2: 227 peptides, 33 chains. Longest chain 15 peptides. Score 0.490 Round 3: 216 peptides, 27 chains. Longest chain 27 peptides. Score 0.534 Round 4: 220 peptides, 26 chains. Longest chain 20 peptides. Score 0.557 Round 5: 222 peptides, 25 chains. Longest chain 29 peptides. Score 0.573 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 197, Estimated correctness of the model 3.8 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6389 reflections ( 99.72 % complete ) and 6513 restraints for refining 2916 atoms. 5686 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2393 (Rfree = 0.000) for 2916 atoms. Found 0 (16 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2285 (Rfree = 0.000) for 2898 atoms. Found 0 (16 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 2886 atoms. Found 0 (16 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2170 (Rfree = 0.000) for 2870 atoms. TimeTaking 54.13