Mon 24 Dec 07:51:02 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 2fur-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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/2fur-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 07:51:06 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/2fur-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 273 and 0 Target number of residues in the AU: 273 Target solvent content: 0.6368 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 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: 55.473 3.200 Wilson plot Bfac: 69.88 7113 reflections ( 99.69 % complete ) and 0 restraints for refining 3735 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3070 (Rfree = 0.000) for 3735 atoms. Found 33 (33 requested) and removed 62 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3782 seeds are put forward NCS extension: 0 residues added, 3782 seeds are put forward Round 1: 165 peptides, 31 chains. Longest chain 10 peptides. Score 0.350 Round 2: 219 peptides, 32 chains. Longest chain 17 peptides. Score 0.534 Round 3: 225 peptides, 31 chains. Longest chain 17 peptides. Score 0.567 Round 4: 250 peptides, 32 chains. Longest chain 19 peptides. Score 0.627 Round 5: 256 peptides, 31 chains. Longest chain 19 peptides. Score 0.655 Taking the results from Round 5 Chains 33, Residues 225, Estimated correctness of the model 55.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6511 restraints for refining 3050 atoms. 5539 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2467 (Rfree = 0.000) for 3050 atoms. Found 21 (27 requested) and removed 39 (13 requested) atoms. Cycle 2: After refmac, R = 0.2187 (Rfree = 0.000) for 2988 atoms. Found 13 (27 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2121 (Rfree = 0.000) for 2980 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2107 (Rfree = 0.000) for 2969 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2070 (Rfree = 0.000) for 2958 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3065 seeds are put forward Round 1: 232 peptides, 32 chains. Longest chain 18 peptides. Score 0.575 Round 2: 269 peptides, 29 chains. Longest chain 23 peptides. Score 0.708 Round 3: 254 peptides, 29 chains. Longest chain 23 peptides. Score 0.673 Round 4: 261 peptides, 28 chains. Longest chain 24 peptides. Score 0.700 Round 5: 259 peptides, 27 chains. Longest chain 24 peptides. Score 0.706 Taking the results from Round 2 Chains 31, Residues 240, Estimated correctness of the model 66.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6551 restraints for refining 3009 atoms. 5589 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 3009 atoms. Found 18 (27 requested) and removed 20 (13 requested) atoms. Cycle 7: After refmac, R = 0.2257 (Rfree = 0.000) for 3004 atoms. Found 5 (25 requested) and removed 14 (13 requested) atoms. Cycle 8: After refmac, R = 0.2230 (Rfree = 0.000) for 2993 atoms. Found 6 (25 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.2204 (Rfree = 0.000) for 2985 atoms. Found 2 (24 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.2188 (Rfree = 0.000) for 2973 atoms. Found 2 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3051 seeds are put forward NCS extension: 39 residues added (4 deleted due to clashes), 3090 seeds are put forward Round 1: 227 peptides, 33 chains. Longest chain 18 peptides. Score 0.546 Round 2: 244 peptides, 31 chains. Longest chain 21 peptides. Score 0.623 Round 3: 267 peptides, 35 chains. Longest chain 18 peptides. Score 0.637 Round 4: 272 peptides, 32 chains. Longest chain 26 peptides. Score 0.683 Round 5: 278 peptides, 26 chains. Longest chain 28 peptides. Score 0.755 Taking the results from Round 5 Chains 27, Residues 252, Estimated correctness of the model 76.0 % 2 chains (30 residues) have been docked in sequence Building loops using Loopy2018 27 chains (252 residues) following loop building 2 chains (30 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6407 restraints for refining 3052 atoms. 5319 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2343 (Rfree = 0.000) for 3052 atoms. Found 16 (24 requested) and removed 20 (13 requested) atoms. Cycle 12: After refmac, R = 0.2190 (Rfree = 0.000) for 3036 atoms. Found 9 (24 requested) and removed 13 (13 requested) atoms. Cycle 13: After refmac, R = 0.2121 (Rfree = 0.000) for 3029 atoms. Found 4 (23 requested) and removed 13 (13 requested) atoms. Cycle 14: After refmac, R = 0.2113 (Rfree = 0.000) for 3016 atoms. Found 2 (23 requested) and removed 14 (13 requested) atoms. Cycle 15: After refmac, R = 0.2113 (Rfree = 0.000) for 3002 atoms. Found 2 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3071 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3092 seeds are put forward Round 1: 229 peptides, 34 chains. Longest chain 18 peptides. Score 0.538 Round 2: 260 peptides, 31 chains. Longest chain 25 peptides. Score 0.665 Round 3: 258 peptides, 33 chains. Longest chain 24 peptides. Score 0.637 Round 4: 250 peptides, 28 chains. Longest chain 20 peptides. Score 0.674 Round 5: 253 peptides, 30 chains. Longest chain 21 peptides. Score 0.659 Taking the results from Round 4 Chains 28, Residues 222, Estimated correctness of the model 59.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6918 restraints for refining 3052 atoms. 6058 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2296 (Rfree = 0.000) for 3052 atoms. Found 22 (22 requested) and removed 16 (13 requested) atoms. Cycle 17: After refmac, R = 0.2125 (Rfree = 0.000) for 3056 atoms. Found 11 (22 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.2018 (Rfree = 0.000) for 3051 atoms. Found 5 (22 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2002 (Rfree = 0.000) for 3041 atoms. Found 3 (22 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.1965 (Rfree = 0.000) for 3026 atoms. Found 9 (22 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 23 residues added (9 deleted due to clashes), 3100 seeds are put forward Round 1: 223 peptides, 35 chains. Longest chain 17 peptides. Score 0.504 Round 2: 248 peptides, 27 chains. Longest chain 24 peptides. Score 0.680 Round 3: 264 peptides, 29 chains. Longest chain 34 peptides. Score 0.696 Round 4: 252 peptides, 26 chains. Longest chain 30 peptides. Score 0.701 Round 5: 252 peptides, 26 chains. Longest chain 29 peptides. Score 0.701 Taking the results from Round 5 Chains 26, Residues 226, Estimated correctness of the model 65.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6828 restraints for refining 3053 atoms. 5950 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2342 (Rfree = 0.000) for 3053 atoms. Found 22 (22 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.2201 (Rfree = 0.000) for 3052 atoms. Found 12 (21 requested) and removed 18 (13 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 3045 atoms. Found 8 (21 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.2125 (Rfree = 0.000) for 3038 atoms. Found 5 (20 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.2153 (Rfree = 0.000) for 3025 atoms. Found 2 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3072 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 3106 seeds are put forward Round 1: 202 peptides, 33 chains. Longest chain 20 peptides. Score 0.461 Round 2: 227 peptides, 31 chains. Longest chain 21 peptides. Score 0.573 Round 3: 222 peptides, 29 chains. Longest chain 21 peptides. Score 0.585 Round 4: 236 peptides, 29 chains. Longest chain 26 peptides. Score 0.626 Round 5: 235 peptides, 31 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 4 Chains 29, Residues 207, Estimated correctness of the model 47.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6754 restraints for refining 3053 atoms. 5934 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2301 (Rfree = 0.000) for 3053 atoms. Found 19 (19 requested) and removed 16 (13 requested) atoms. Cycle 27: After refmac, R = 0.2127 (Rfree = 0.000) for 3050 atoms. Found 13 (19 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.2065 (Rfree = 0.000) for 3041 atoms. Found 10 (19 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 3035 atoms. Found 6 (19 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1888 (Rfree = 0.000) for 3023 atoms. Found 5 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3079 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3107 seeds are put forward Round 1: 197 peptides, 32 chains. Longest chain 15 peptides. Score 0.458 Round 2: 211 peptides, 27 chains. Longest chain 23 peptides. Score 0.579 Round 3: 221 peptides, 27 chains. Longest chain 23 peptides. Score 0.609 Round 4: 217 peptides, 26 chains. Longest chain 23 peptides. Score 0.610 Round 5: 216 peptides, 25 chains. Longest chain 21 peptides. Score 0.621 Taking the results from Round 5 Chains 26, Residues 191, Estimated correctness of the model 46.6 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6700 restraints for refining 3053 atoms. 5889 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2123 (Rfree = 0.000) for 3053 atoms. Found 18 (19 requested) and removed 15 (13 requested) atoms. Cycle 32: After refmac, R = 0.2011 (Rfree = 0.000) for 3053 atoms. Found 10 (19 requested) and removed 18 (13 requested) atoms. Cycle 33: After refmac, R = 0.1997 (Rfree = 0.000) for 3042 atoms. Found 11 (19 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1969 (Rfree = 0.000) for 3037 atoms. Found 7 (19 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.1978 (Rfree = 0.000) for 3027 atoms. Found 9 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3095 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3121 seeds are put forward Round 1: 180 peptides, 28 chains. Longest chain 17 peptides. Score 0.460 Round 2: 199 peptides, 26 chains. Longest chain 24 peptides. Score 0.556 Round 3: 203 peptides, 25 chains. Longest chain 26 peptides. Score 0.582 Round 4: 211 peptides, 28 chains. Longest chain 17 peptides. Score 0.565 Round 5: 204 peptides, 27 chains. Longest chain 21 peptides. Score 0.557 Taking the results from Round 3 Chains 25, Residues 178, Estimated correctness of the model 36.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 7047 restraints for refining 3052 atoms. 6360 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2158 (Rfree = 0.000) for 3052 atoms. Found 17 (19 requested) and removed 16 (13 requested) atoms. Cycle 37: After refmac, R = 0.2087 (Rfree = 0.000) for 3051 atoms. Found 9 (19 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2054 (Rfree = 0.000) for 3047 atoms. Found 5 (19 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2054 (Rfree = 0.000) for 3039 atoms. Found 2 (19 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 3027 atoms. Found 5 (19 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3128 seeds are put forward Round 1: 162 peptides, 27 chains. Longest chain 16 peptides. Score 0.408 Round 2: 189 peptides, 24 chains. Longest chain 18 peptides. Score 0.553 Round 3: 186 peptides, 25 chains. Longest chain 17 peptides. Score 0.528 Round 4: 199 peptides, 23 chains. Longest chain 18 peptides. Score 0.598 Round 5: 199 peptides, 26 chains. Longest chain 18 peptides. Score 0.556 Taking the results from Round 4 Chains 25, Residues 176, Estimated correctness of the model 40.5 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6663 restraints for refining 3053 atoms. 5888 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2284 (Rfree = 0.000) for 3053 atoms. Found 19 (19 requested) and removed 22 (13 requested) atoms. Cycle 42: After refmac, R = 0.2149 (Rfree = 0.000) for 3047 atoms. Found 14 (19 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2125 (Rfree = 0.000) for 3047 atoms. Found 11 (19 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.2102 (Rfree = 0.000) for 3042 atoms. Found 7 (19 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2100 (Rfree = 0.000) for 3036 atoms. Found 5 (19 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3122 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 13 peptides. Score 0.422 Round 2: 184 peptides, 26 chains. Longest chain 16 peptides. Score 0.506 Round 3: 179 peptides, 25 chains. Longest chain 20 peptides. Score 0.504 Round 4: 172 peptides, 21 chains. Longest chain 18 peptides. Score 0.542 Round 5: 176 peptides, 28 chains. Longest chain 14 peptides. Score 0.445 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 151, Estimated correctness of the model 24.5 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2fur-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (151 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7113 reflections ( 99.69 % complete ) and 6854 restraints for refining 3053 atoms. 6199 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2226 (Rfree = 0.000) for 3053 atoms. Found 0 (19 requested) and removed 3 (13 requested) atoms. Cycle 47: After refmac, R = 0.2182 (Rfree = 0.000) for 3047 atoms. Found 0 (19 requested) and removed 5 (13 requested) atoms. Cycle 48: After refmac, R = 0.2221 (Rfree = 0.000) for 3040 atoms. Found 0 (19 requested) and removed 5 (13 requested) atoms. Cycle 49: After refmac, R = 0.2357 (Rfree = 0.000) for 3035 atoms. Found 0 (19 requested) and removed 13 (13 requested) atoms. Writing output files ... TimeTaking 35.2