Mon 24 Dec 01:05:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pr7-1.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-1.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-1.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-parrot-mrncs ############### 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 01:05:58 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-parrot-mrncs/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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.4668 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-1.4-parrot-mrncs.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: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-1.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.40 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.053 1.440 Wilson plot Bfac: 17.25 40620 reflections ( 79.26 % complete ) and 0 restraints for refining 2445 atoms. Observations/parameters ratio is 4.15 ------------------------------------------------------ Starting model: R = 0.3263 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2735 (Rfree = 0.000) for 2445 atoms. Found 126 (213 requested) and removed 116 (106 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.72 1.74 Round 1: 221 peptides, 17 chains. Longest chain 39 peptides. Score 0.822 Round 2: 250 peptides, 7 chains. Longest chain 61 peptides. Score 0.932 Round 3: 253 peptides, 6 chains. Longest chain 62 peptides. Score 0.940 Round 4: 259 peptides, 6 chains. Longest chain 71 peptides. Score 0.944 Round 5: 264 peptides, 6 chains. Longest chain 73 peptides. Score 0.947 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2496 restraints for refining 2300 atoms. 613 conditional restraints added. Observations/parameters ratio is 4.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2768 (Rfree = 0.000) for 2300 atoms. Found 123 (200 requested) and removed 22 (100 requested) atoms. Cycle 2: After refmac, R = 0.2471 (Rfree = 0.000) for 2401 atoms. Found 96 (209 requested) and removed 17 (104 requested) atoms. Cycle 3: After refmac, R = 0.2324 (Rfree = 0.000) for 2475 atoms. Found 71 (216 requested) and removed 9 (108 requested) atoms. Cycle 4: After refmac, R = 0.2217 (Rfree = 0.000) for 2530 atoms. Found 74 (221 requested) and removed 8 (110 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 2587 atoms. Found 61 (226 requested) and removed 12 (113 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 3: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Round 4: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 5: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2516 restraints for refining 2473 atoms. 541 conditional restraints added. Observations/parameters ratio is 4.11 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2242 (Rfree = 0.000) for 2473 atoms. Found 99 (216 requested) and removed 15 (108 requested) atoms. Cycle 7: After refmac, R = 0.2147 (Rfree = 0.000) for 2554 atoms. Found 81 (223 requested) and removed 7 (111 requested) atoms. Cycle 8: After refmac, R = 0.2096 (Rfree = 0.000) for 2622 atoms. Found 66 (229 requested) and removed 9 (114 requested) atoms. Cycle 9: After refmac, R = 0.2035 (Rfree = 0.000) for 2677 atoms. Found 44 (234 requested) and removed 17 (117 requested) atoms. Cycle 10: After refmac, R = 0.1976 (Rfree = 0.000) for 2699 atoms. Found 63 (236 requested) and removed 9 (118 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 265 peptides, 5 chains. Longest chain 73 peptides. Score 0.952 Round 3: 265 peptides, 6 chains. Longest chain 62 peptides. Score 0.947 Round 4: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Round 5: 264 peptides, 6 chains. Longest chain 63 peptides. Score 0.947 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2652 restraints for refining 2572 atoms. 677 conditional restraints added. Observations/parameters ratio is 3.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2143 (Rfree = 0.000) for 2572 atoms. Found 122 (224 requested) and removed 18 (112 requested) atoms. Cycle 12: After refmac, R = 0.2089 (Rfree = 0.000) for 2672 atoms. Found 67 (233 requested) and removed 10 (116 requested) atoms. Cycle 13: After refmac, R = 0.2020 (Rfree = 0.000) for 2722 atoms. Found 64 (238 requested) and removed 8 (119 requested) atoms. Cycle 14: After refmac, R = 0.1965 (Rfree = 0.000) for 2773 atoms. Found 67 (242 requested) and removed 15 (121 requested) atoms. Cycle 15: After refmac, R = 0.1943 (Rfree = 0.000) for 2819 atoms. Found 61 (246 requested) and removed 27 (123 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 3: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 4: 264 peptides, 6 chains. Longest chain 62 peptides. Score 0.947 Round 5: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2738 restraints for refining 2642 atoms. 763 conditional restraints added. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2096 (Rfree = 0.000) for 2642 atoms. Found 135 (230 requested) and removed 14 (115 requested) atoms. Cycle 17: After refmac, R = 0.2047 (Rfree = 0.000) for 2760 atoms. Found 78 (241 requested) and removed 12 (120 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 2822 atoms. Found 45 (246 requested) and removed 3 (123 requested) atoms. Cycle 19: After refmac, R = 0.1924 (Rfree = 0.000) for 2860 atoms. Found 43 (250 requested) and removed 8 (125 requested) atoms. Cycle 20: After refmac, R = 0.1889 (Rfree = 0.000) for 2882 atoms. Found 47 (252 requested) and removed 11 (126 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 2: 265 peptides, 5 chains. Longest chain 72 peptides. Score 0.952 Round 3: 265 peptides, 5 chains. Longest chain 74 peptides. Score 0.952 Round 4: 264 peptides, 6 chains. Longest chain 72 peptides. Score 0.947 Round 5: 265 peptides, 6 chains. Longest chain 65 peptides. Score 0.947 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2840 restraints for refining 2701 atoms. 883 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2092 (Rfree = 0.000) for 2701 atoms. Found 133 (235 requested) and removed 15 (117 requested) atoms. Cycle 22: After refmac, R = 0.2007 (Rfree = 0.000) for 2814 atoms. Found 65 (246 requested) and removed 8 (123 requested) atoms. Cycle 23: After refmac, R = 0.1960 (Rfree = 0.000) for 2861 atoms. Found 60 (250 requested) and removed 16 (125 requested) atoms. Cycle 24: After refmac, R = 0.1909 (Rfree = 0.000) for 2900 atoms. Found 58 (253 requested) and removed 12 (126 requested) atoms. Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 2938 atoms. Found 53 (257 requested) and removed 18 (128 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 2: 266 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 3: 265 peptides, 5 chains. Longest chain 74 peptides. Score 0.952 Round 4: 264 peptides, 7 chains. Longest chain 72 peptides. Score 0.942 Round 5: 264 peptides, 6 chains. Longest chain 73 peptides. Score 0.947 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2891 restraints for refining 2728 atoms. 928 conditional restraints added. Observations/parameters ratio is 3.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2094 (Rfree = 0.000) for 2728 atoms. Found 136 (238 requested) and removed 13 (119 requested) atoms. Cycle 27: After refmac, R = 0.2024 (Rfree = 0.000) for 2847 atoms. Found 73 (249 requested) and removed 8 (124 requested) atoms. Cycle 28: After refmac, R = 0.1953 (Rfree = 0.000) for 2900 atoms. Found 65 (254 requested) and removed 12 (127 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 2940 atoms. Found 67 (258 requested) and removed 10 (129 requested) atoms. Cycle 30: After refmac, R = 0.1882 (Rfree = 0.000) for 2991 atoms. Found 57 (261 requested) and removed 23 (130 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 4 chains. Longest chain 74 peptides. Score 0.957 Round 2: 264 peptides, 5 chains. Longest chain 72 peptides. Score 0.951 Round 3: 266 peptides, 5 chains. Longest chain 84 peptides. Score 0.953 Round 4: 265 peptides, 6 chains. Longest chain 61 peptides. Score 0.947 Round 5: 264 peptides, 6 chains. Longest chain 72 peptides. Score 0.947 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2932 restraints for refining 2784 atoms. 966 conditional restraints added. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2067 (Rfree = 0.000) for 2784 atoms. Found 135 (243 requested) and removed 16 (121 requested) atoms. Cycle 32: After refmac, R = 0.2000 (Rfree = 0.000) for 2902 atoms. Found 60 (253 requested) and removed 18 (126 requested) atoms. Cycle 33: After refmac, R = 0.1952 (Rfree = 0.000) for 2933 atoms. Found 61 (257 requested) and removed 10 (128 requested) atoms. Cycle 34: After refmac, R = 0.1895 (Rfree = 0.000) for 2972 atoms. Found 54 (260 requested) and removed 18 (130 requested) atoms. Cycle 35: After refmac, R = 0.1862 (Rfree = 0.000) for 2998 atoms. Found 56 (262 requested) and removed 11 (131 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 4 chains. Longest chain 74 peptides. Score 0.957 Round 2: 262 peptides, 5 chains. Longest chain 72 peptides. Score 0.950 Round 3: 266 peptides, 5 chains. Longest chain 84 peptides. Score 0.953 Round 4: 263 peptides, 8 chains. Longest chain 62 peptides. Score 0.937 Round 5: 261 peptides, 6 chains. Longest chain 74 peptides. Score 0.945 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2983 restraints for refining 2813 atoms. 1017 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2042 (Rfree = 0.000) for 2813 atoms. Found 147 (245 requested) and removed 12 (122 requested) atoms. Cycle 37: After refmac, R = 0.1984 (Rfree = 0.000) for 2938 atoms. Found 72 (257 requested) and removed 9 (128 requested) atoms. Cycle 38: After refmac, R = 0.1918 (Rfree = 0.000) for 2993 atoms. Found 54 (262 requested) and removed 15 (131 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 3021 atoms. Found 48 (264 requested) and removed 12 (132 requested) atoms. Cycle 40: After refmac, R = 0.1828 (Rfree = 0.000) for 3048 atoms. Found 56 (267 requested) and removed 12 (133 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 4 chains. Longest chain 74 peptides. Score 0.957 Round 2: 263 peptides, 4 chains. Longest chain 135 peptides. Score 0.956 Round 3: 259 peptides, 5 chains. Longest chain 72 peptides. Score 0.949 Round 4: 262 peptides, 8 chains. Longest chain 59 peptides. Score 0.936 Round 5: 261 peptides, 5 chains. Longest chain 69 peptides. Score 0.950 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 3027 restraints for refining 2807 atoms. 1061 conditional restraints added. Observations/parameters ratio is 3.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2064 (Rfree = 0.000) for 2807 atoms. Found 151 (245 requested) and removed 23 (122 requested) atoms. Cycle 42: After refmac, R = 0.1990 (Rfree = 0.000) for 2929 atoms. Found 78 (256 requested) and removed 10 (128 requested) atoms. Cycle 43: After refmac, R = 0.1920 (Rfree = 0.000) for 2988 atoms. Found 68 (261 requested) and removed 11 (130 requested) atoms. Cycle 44: After refmac, R = 0.1880 (Rfree = 0.000) for 3036 atoms. Found 72 (266 requested) and removed 12 (133 requested) atoms. Cycle 45: After refmac, R = 0.1852 (Rfree = 0.000) for 3086 atoms. Found 69 (270 requested) and removed 29 (135 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.66 1.68 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 3: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 4: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 5: 260 peptides, 8 chains. Longest chain 59 peptides. Score 0.934 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pr7-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 40620 reflections ( 79.26 % complete ) and 2999 restraints for refining 2809 atoms. 1041 conditional restraints added. Observations/parameters ratio is 3.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2087 (Rfree = 0.000) for 2809 atoms. Found 0 (245 requested) and removed 4 (122 requested) atoms. Cycle 47: After refmac, R = 0.1991 (Rfree = 0.000) for 2798 atoms. Found 0 (240 requested) and removed 0 (122 requested) atoms. Cycle 48: After refmac, R = 0.1933 (Rfree = 0.000) for 2792 atoms. Found 0 (239 requested) and removed 0 (122 requested) atoms. Cycle 49: After refmac, R = 0.1904 (Rfree = 0.000) for 2786 atoms. TimeTaking 37.75